Alignments for a candidate for putA in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Marivita geojedonensis DPG-138

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_085640383.1 MGEO_RS16525 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::Phaeo:GFF1160
         (1158 letters)



>NCBI__GCF_002115805.1:WP_085640383.1
          Length = 1140

 Score = 1503 bits (3892), Expect = 0.0
 Identities = 788/1137 (69%), Positives = 890/1137 (78%), Gaps = 11/1137 (0%)

Query: 24   LRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISANAAALVRDIRGHSSPGLMEVFLAE 83
            LR  ID  TY D+A   D L A A L  TDR  I A A  LV +IR  S PGLMEVFL+E
Sbjct: 9    LRPLIDDNTYADEALKVDSLRATAQLTQTDRDAIKARATKLVTEIREDSRPGLMEVFLSE 68

Query: 84   YGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAPSEWGKHLGKSTSSLVNASTWALM 143
            YGLST+EG+ALMCLAEALLRVPDA TIDALIEDKIAPS W  HLG+STS LVNASTWALM
Sbjct: 69   YGLSTEEGIALMCLAEALLRVPDAATIDALIEDKIAPSNWASHLGESTSPLVNASTWALM 128

Query: 144  LTGKVL-DEKRSPVSALRGAMKRLGEPVIRTAVSRAMKEMGRQFVLGETIEGAMKRAAGM 202
            LTGKVL DE+  PV  LRGA+KRLGEPVIRTAV RAMKEMG QFVLGETI+ AMKRAA M
Sbjct: 129  LTGKVLKDEQPGPVGHLRGAIKRLGEPVIRTAVGRAMKEMGAQFVLGETIQSAMKRAARM 188

Query: 203  EAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAAACNSADIRQNPGISVKLSALHP 262
            EAKGYTYSYDMLGEAARTE DA RYHL+YSRAISAIA A  S DIR NPGISVKLSALHP
Sbjct: 189  EAKGYTYSYDMLGEAARTETDARRYHLSYSRAISAIAEAAKSKDIRDNPGISVKLSALHP 248

Query: 263  RYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEEADRLSLSLEVIEEVISDPALAG 322
            RYE AQ+ +V  ++VPRL+ LA LA++AG+GLN+DAEEADRLS+SL+VIE V+S+P+L G
Sbjct: 249  RYEEAQQDTVMNEVVPRLRTLAQLARSAGIGLNIDAEEADRLSVSLDVIETVLSEPSLKG 308

Query: 323  WDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLVKGAYWDTEVKRAQVEGVDGFPV 382
            WDGFGVVVQAYGPR G  +D LY++A R DR++MVRLVKGAYWDTE+KRAQV G+  FPV
Sbjct: 309  WDGFGVVVQAYGPRAGHVIDWLYNLAERLDRKIMVRLVKGAYWDTEIKRAQVAGLPAFPV 368

Query: 383  FTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVSAILHMAKDTDKGAYEFQRLHGM 442
            FT K  TD+SYIANARKLL +TDRIYPQFATHNAHTV+AILHMA+D  +  +EFQRLHGM
Sbjct: 369  FTAKHHTDISYIANARKLLGMTDRIYPQFATHNAHTVAAILHMAED--RTLFEFQRLHGM 426

Query: 443  GETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDENVPPELVA 502
            GE LH++V +   T CRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVD +VP   VA
Sbjct: 427  GEALHDIVKDDEGTRCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDTDVPAAEVA 486

Query: 503  ADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPTLAAIDAARAPWKSHSWAAEPLL 562
            ADPF         L  GP+LF PERPNS G+DL H PT AAI+AAR P+    W A PL+
Sbjct: 487  ADPFDT--QAVPKLPTGPELFAPERPNSKGWDLTHRPTRAAIEAARKPFSGVQWTATPLV 544

Query: 563  AKAPETATTTDEPVRNPADL-TTVGRVQTAGQAEIETALSAATPWNASAETRAEVLNRAA 621
            A   ET  T  +PV NPA    TVG V  A    + TA + ATPWNA A  RAEVLN+AA
Sbjct: 545  AGDAETGAT--DPVINPARPGDTVGSVTWATSGTVATACTVATPWNADAAERAEVLNKAA 602

Query: 622  DLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYYAARISAEPPVGVFTCISPWNF 681
            DLYEA+YGELFALL REAGK+L D VAELREAVDFLRYYAAR     P GVF CISPWNF
Sbjct: 603  DLYEAHYGELFALLAREAGKSLLDAVAELREAVDFLRYYAARAEGPDPQGVFACISPWNF 662

Query: 682  PLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLHEAGVPRSALQLLPGAGAVGGA 741
            PLAIF+GQIAAAL  GNAVLAKPAEQTPLIA+RA+ LLHEAGVP +ALQLLPGAG VG A
Sbjct: 663  PLAIFTGQIAAALTTGNAVLAKPAEQTPLIAYRAVQLLHEAGVPTTALQLLPGAGDVGAA 722

Query: 742  LTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAETGGLNAMIVDSTALPEQAVQS 801
            LTS+  V GVAFTGST TA  I  +MA+HL PGAPLIAETGGLNAMIVDSTALPEQAVQ+
Sbjct: 723  LTSNPAVKGVAFTGSTETAQIIHRSMAKHLAPGAPLIAETGGLNAMIVDSTALPEQAVQA 782

Query: 802  IIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDALHLGDPWNLSTDSGPVIDETA 861
            I+ESAFQSAGQRCSALRCLY+QEDIA++ ++ML GAMDAL +GDPW   TD GP ID  A
Sbjct: 783  IVESAFQSAGQRCSALRCLYVQEDIAESFVEMLTGAMDALVIGDPWIYGTDVGPAIDAEA 842

Query: 862  RAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITGIQALEQEIFGPVLHVVRFKSQ 921
            R GI++++DAA  EGRVL  +  P GGTFV PTLI ++GI  LE+EIFGPVLH+  FKS+
Sbjct: 843  RDGIISYVDAAEVEGRVLHRLPLPGGGTFVPPTLIRVSGIADLEREIFGPVLHIATFKSK 902

Query: 922  DLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGNLYVNRNQIGAIVGSQPFGGEG 981
            D+D +I  IN T YGLTFGL TRIDDRVQ++ ++I AGN+YVNRNQIGAIVGSQPFGGEG
Sbjct: 903  DIDTVIDAINGTDYGLTFGLQTRIDDRVQHVSEQIKAGNIYVNRNQIGAIVGSQPFGGEG 962

Query: 982  LSGTGPKAGGPFYMMRFCAPDRQKSVDSWPS--DAPAMTMLPAPTGQPMQEITTSLPGPT 1039
            LSGTGPKAGGP Y+ RF       + D WPS      +T      G       T+LPGPT
Sbjct: 963  LSGTGPKAGGPNYLARFRRHPADTAGDVWPSQDSKDRLTKALTSAGGKASATKTTLPGPT 1022

Query: 1040 GESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEATGPLDMRQLLTMEGTSGVI 1099
            GESN L+ +AR P+LCLGPGP+A  AQARAV ALGG A++A G +    L  +E + G I
Sbjct: 1023 GESNVLTAMARGPILCLGPGPEAAKAQARAVEALGGIAVKAEGGIAPDWLADLE-SEGAI 1081

Query: 1100 WWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHVCVDTTAAGGNAALLGG 1156
            WWGD+ TAR + + LA R GPILPLI G+PDK     ERHVCVDTTA+GGNA LL G
Sbjct: 1082 WWGDDETARALRTELASRKGPILPLITGMPDKGHACHERHVCVDTTASGGNAQLLSG 1138


Lambda     K      H
   0.317    0.132    0.387 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3260
Number of extensions: 147
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1158
Length of database: 1140
Length adjustment: 46
Effective length of query: 1112
Effective length of database: 1094
Effective search space:  1216528
Effective search space used:  1216528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)

Align candidate WP_085640383.1 MGEO_RS16525 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01238.hmm
# target sequence database:        /tmp/gapView.719781.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-187  609.6   0.1   3.8e-186  605.4   0.1    2.8  4  NCBI__GCF_002115805.1:WP_085640383.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085640383.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.13      0.13      96     145 ..      43      90 ..      16     129 .. 0.63
   2 ?   -2.4   0.0     0.068     0.068       7      95 ..     274     374 ..     271     394 .. 0.69
   3 !  605.4   0.1  3.8e-186  3.8e-186       1     497 [.     503     981 ..     503     984 .. 0.97
   4 ?    0.2   0.0     0.011     0.011     240     271 ..    1077    1108 ..    1064    1128 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.13
                             TIGR01238  96 keraailerladlleshmpelvallvreaGktlsnaiaevreavdflryy 145
                                           k ra++   ++++ e   p l+ +   e G + ++ ia +  a  +lr  
  NCBI__GCF_002115805.1:WP_085640383.1  43 KARATK--LVTEIREDSRPGLMEVFLSEYGLSTEEGIALMCLAEALLRVP 90 
                                           333333..356777999999999999999999999998776666666654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.068
                             TIGR01238   7 rknslGvdlanese......lksleeqllkaaakkfqaapivgeka..kaegeaqpvknpa...drkdivGqv 68 
                                           r+   G++++ e+       l+ +e+ l +  +k ++   +v + +  +a + ++ + n a   drk++v  v
  NCBI__GCF_002115805.1:WP_085640383.1 274 RSAGIGLNIDAEEAdrlsvsLDVIETVLSEPSLKGWDGFGVVVQAYgpRAGHVIDWLYNLAerlDRKIMVRLV 346
                                           6667778887775322221245566777778889999999887666668888888777765222667888888 PP

                             TIGR01238  69 sead.aaevqeavdsavaafaewsatda 95 
                                           + a  + e+++a  + + af++++a   
  NCBI__GCF_002115805.1:WP_085640383.1 347 KGAYwDTEIKRAQVAGLPAFPVFTAKHH 374
                                           8886255788888888889998888765 PP

  == domain 3  score: 605.4 bits;  conditional E-value: 3.8e-186
                             TIGR01238   1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseada 73 
                                           +l++  r ns+G dl+   + + +e+  +     ++ a p+v+++  + g ++pv npa + d vG v+ a  
  NCBI__GCF_002115805.1:WP_085640383.1 503 ELFAPERPNSKGWDLTHRPTRAAIEAARKPFSGVQWTATPLVAGD-AETGATDPVINPARPGDTVGSVTWATS 574
                                           699999************************************655.57899********************99 PP

                             TIGR01238  74 aevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryya 146
                                            +v  a +     ++ w+a da+era +l+++adl e h  el all reaGk+l +a+ae+reavdflryya
  NCBI__GCF_002115805.1:WP_085640383.1 575 GTVATACTV----ATPWNA-DAAERAEVLNKAADLYEAHYGELFALLAREAGKSLLDAVAELREAVDFLRYYA 642
                                           888777665....467998.899************************************************** PP

                             TIGR01238 147 kqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagv 219
                                            ++      e   ++G++ cispwnfplaiftGqiaaal++Gn+v+akpaeqt+lia+rav+ll+eaGvp+++
  NCBI__GCF_002115805.1:WP_085640383.1 643 ARA------EGPDPQGVFACISPWNFPLAIFTGQIAAALTTGNAVLAKPAEQTPLIAYRAVQLLHEAGVPTTA 709
                                           *99......456799********************************************************** PP

                             TIGR01238 220 iqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvva 292
                                           +qllpG+G+ vGaalts+++++Gv+ftGste+a+ i++++ak  ++ +pliaetGG namivdstal+eq v+
  NCBI__GCF_002115805.1:WP_085640383.1 710 LQLLPGAGD-VGAALTSNPAVKGVAFTGSTETAQIIHRSMAKHLAPGAPLIAETGGLNAMIVDSTALPEQAVQ 781
                                           ********9.*************************************************************** PP

                             TIGR01238 293 dvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmk 365
                                            +++saf+saGqrcsalr l+vqed+a+  ++++ Gamd l++g p  + tdvGp idaea++ + +++++ +
  NCBI__GCF_002115805.1:WP_085640383.1 782 AIVESAFQSAGQRCSALRCLYVQEDIAESFVEMLTGAMDALVIGDPWIYGTDVGPAIDAEARDGIISYVDAAE 854
                                           ************************************************************************* PP

                             TIGR01238 366 akakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGv 438
                                             ++ ++++ l        gtfv+ptl+ +  +++l++e+fGpvlh+  +k++++d v+d in + yglt+G+
  NCBI__GCF_002115805.1:WP_085640383.1 855 VEGRVLHRLPLPG-----GGTFVPPTLIRVSGIADLEREIFGPVLHIATFKSKDIDTVIDAINGTDYGLTFGL 922
                                           *********9998.....8****************************************************** PP

                             TIGR01238 439 hsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497
                                            +ri++ v+++ +++k+Gn+yvnrn++Ga+vG qpfGGeGlsGtGpkaGGp yl r+ r
  NCBI__GCF_002115805.1:WP_085640383.1 923 QTRIDDRVQHVSEQIKAGNIYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPNYLARFRR 981
                                           ********************************************************987 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.011
                             TIGR01238  240 iaGviftGstevarlinkalakredapvplia 271 
                                             +G i+ G  e+ar ++ +la+r+ +  pli+
  NCBI__GCF_002115805.1:WP_085640383.1 1077 SEGAIWWGDDETARALRTELASRKGPILPLIT 1108
                                            5799999*******************999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1140 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 43.80
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources