Alignments for a candidate for putA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Dinoroseobacter shibae DFL-12

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 3608920 Dshi_2311 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= reanno::Marino:GFF2744
         (1209 letters)



>FitnessBrowser__Dino:3608920
          Length = 1221

 Score = 1263 bits (3267), Expect = 0.0
 Identities = 665/1209 (55%), Positives = 848/1209 (70%), Gaps = 19/1209 (1%)

Query: 15   RQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRKNAKSTIMEKFLAEY 74
            R  +R +Y A+E  ++  + A  +LS  ER+  +A  A  V  VR   + ++ME FLAEY
Sbjct: 16   RAQVRAHYTAEETALLKSLAARIKLSAHEREKAAAAGARYVTRVRNETRPSMMEAFLAEY 75

Query: 75   GLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKASSGLINTATVALLM 134
            GL+T EGV LMCLAEALLRVPD  TI +LIEDK+    WG H+G +SS L+N +T AL++
Sbjct: 76   GLSTSEGVGLMCLAEALLRVPDADTIDDLIEDKVAPSNWGAHLGHSSSSLVNASTWALML 135

Query: 135  TSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVLGRDIDEAQDEAKEY 194
            T  +L +  R      LR L+KR GEPV+RT  GQ+MK +GRQFVLG+ I+E    A+E 
Sbjct: 136  TGKVLDEDPRGPA-RALRGLVKRLGEPVVRTAVGQSMKVLGRQFVLGQTIEEGLKNAREL 194

Query: 195  MAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKGDVRKNPGISVKLSALLAR 254
              KG+TYSYDMLGEAARTD DA+RY+ +Y+ AI +IA+ + GDVR +PGISVKLSAL  R
Sbjct: 195  EKKGFTYSYDMLGEAARTDADARRYHAAYAQAITAIARQATGDVRSSPGISVKLSALHPR 254

Query: 255  YEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLDVIEELVADPELAGW 314
            YEY ++  VM +L+PRA  LVK+AA A +GFN+DAEEQDRLDLSLDVIE +++DP+L GW
Sbjct: 255  YEYTHRHSVMADLVPRAAALVKQAAQAGIGFNVDAEEQDRLDLSLDVIEAMMSDPDLDGW 314

Query: 315  DGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEIKRAQVMGLNGFPVF 374
            DGFGVVVQAYG+R+  V++ LY +AE+YDRK MVRLVKGAYWD EIK AQ +G+  FPVF
Sbjct: 315  DGFGVVVQAYGRRAGPVIETLYDMAERYDRKIMVRLVKGAYWDTEIKLAQELGVERFPVF 374

Query: 375  TRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTKGVDNYEFQRLHGMG 434
            TRK  +DVS+++CA  LL+  +RIYPQFATHNAH+ +A+L+MA     D +EFQRLHGMG
Sbjct: 375  TRKNNTDVSYMACAQMLLDRRDRIYPQFATHNAHTCAAVLQMAGNAR-DCFEFQRLHGMG 433

Query: 435  ESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVNQIVDKRITPEEIAK 494
             SLH  V +  G  CRIYAPVG H+DLLAYLVRRLLENGANSSFVNQIVD  I  E I+ 
Sbjct: 434  ASLHQIVKETEGTRCRIYAPVGAHQDLLAYLVRRLLENGANSSFVNQIVDPDIPAEAISA 493

Query: 495  DPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEIEKGRGAYKDYRWKG 554
            DP+  +E++G+ I + AI  P  LF   RRNS+G+ + +P ++  +   R A+ +  W  
Sbjct: 494  DPVSEMEKLGDQIPNPAIRQPSDLFAPDRRNSRGYRVNEPASILPLMTAREAFAETTWHA 553

Query: 555  GPLIAGEVAGT-EIQVVRNPADPDDLVGHVTQASDADVDTAITSAAAAFESWSAKSAEER 613
             P++AG    T   + V +PAD   LVG V +AS  DV  A+ +A   F  WSA+   ER
Sbjct: 554  RPMLAGGRDPTGPTREVHSPADKTRLVGTVQEASAEDVACALDAAETGFRDWSARPVSER 613

Query: 614  AACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYYANEAIRYK--DSG 671
            A  +RK+ D+YE+N AEL A+TTREAGK++LD +AE+REAVDF ++YANEA R +  D G
Sbjct: 614  ADMLRKLADMYEDNIAELTAITTREAGKTVLDGIAEVREAVDFLRFYANEAERLEEEDPG 673

Query: 672  DARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAVELMHQAGIPKD 731
              RG+  CISPWNFPLAIFTGQI A L  GN V+AKPAEQT ++A RAV++M   G+P  
Sbjct: 674  RPRGIFVCISPWNFPLAIFTGQIAAALVMGNAVLAKPAEQTPIIAARAVQMMRDCGLPDA 733

Query: 732  AIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDAPLVAETGGLNA 791
            A+QL+PG G  VG  LTSD R++GVCFTGST  A  I+K + +N  P+A LVAETGGLNA
Sbjct: 734  ALQLLPGDGPMVGGPLTSDPRIAGVCFTGSTEVAMIIHKALAKNAGPEAVLVAETGGLNA 793

Query: 792  MIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLYGAMEELGIGDP 851
            MIVDSTAL EQ VRD+L SSFQSAGQRCSALR+LYVQ D+ D L+EML GA++ L IGD 
Sbjct: 794  MIVDSTALHEQAVRDILISSFQSAGQRCSALRILYVQEDVHDKLMEMLSGALDALVIGDS 853

Query: 852  WLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAVLSVSGIEELEE 911
            W L  DV PVID +A+  I+ + ++  + G L+K +  P+ G +V+PA++ V GI ++E 
Sbjct: 854  WNLDVDVSPVIDADAQSDILGYIDQHRKAGTLIKTLAAPDSGTYVTPAIVKVGGIADMER 913

Query: 912  EIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSRIKVGNTYVNRN 971
            EIFGPVLHVATF+A  ID+VVD INA+ YGLTFG+H+R+D RVE+I  RI+VGN YVNRN
Sbjct: 914  EIFGPVLHVATFKANEIDQVVDAINARRYGLTFGLHTRIDDRVEQIVERIQVGNVYVNRN 973

Query: 972  QIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLK-GETVEREADSNARKVDAKQLQKLIG 1030
            QIGAIVGSQPFGGEGLSGTGPKAGGP Y+ RF K G++    A   A  +    L   + 
Sbjct: 974  QIGAIVGSQPFGGEGLSGTGPKAGGPLYLTRFRKVGKSTSHPAPQGA-VLGKAALNTALS 1032

Query: 1031 QLDKLK-ASRPE----ARMDAIRPIFGNVPEPL------DAHVEALPGPTGETNRLSNHA 1079
             LD    A+RP+     RM A+    G V   L      D   + LPGPTGE+NRLS   
Sbjct: 1033 SLDARNWAARPDRVHILRM-ALSGSTGVVRRALSETAAFDMSPQTLPGPTGESNRLSMVP 1091

Query: 1080 RGVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEA 1139
            RG VLCLGP  E A+ QA  AL  G  VV+  PG+  +    + AG P+V   G ++   
Sbjct: 1092 RGTVLCLGPTPEIAMAQAVQALGAGCAVVIALPGSTPLSQPLSDAGAPVVTLDGTVDCVT 1151

Query: 1140 LATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAG 1199
            L  + G E V + G     +  R AL++RDG ++PLI +    +R+V+ERHLC+DTTAAG
Sbjct: 1152 LTELTGIEVVAAAGASDWTRTLRVALSQRDGPIIPLIVDEIAPERYVLERHLCIDTTAAG 1211

Query: 1200 GNASLIAAS 1208
            GNA L+AAS
Sbjct: 1212 GNAKLLAAS 1220


Lambda     K      H
   0.316    0.133    0.378 

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: 3465
Number of extensions: 168
Number of successful extensions: 6
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: 1209
Length of database: 1221
Length adjustment: 47
Effective length of query: 1162
Effective length of database: 1174
Effective search space:  1364188
Effective search space used:  1364188
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 (21.6 bits)
S2: 59 (27.3 bits)

Align candidate 3608920 Dshi_2311 (delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq))
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.28029.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.2e-194  633.4   3.2   7.9e-194  630.7   0.1    2.1  2  lcl|FitnessBrowser__Dino:3608920  Dshi_2311 delta-1-pyrroline-5-ca


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608920  Dshi_2311 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.7   0.1  7.9e-194  7.9e-194       1     498 [.     516    1008 ..     516    1010 .. 0.99
   2 !    2.9   0.6    0.0017    0.0017     158     272 ..    1089    1190 ..    1075    1198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 630.7 bits;  conditional E-value: 7.9e-194
                         TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaae 75  
                                        dl++  r+ns G  ++    + +l +  ++ a+ +++a p++++     g ++ v +pad+  +vG+v+ea+a++
  lcl|FitnessBrowser__Dino:3608920  516 DLFAPDRRNSRGYRVNEPASILPLMTAREAFAETTWHARPMLAGGRDPTGPTREVHSPADKTRLVGTVQEASAED 590 
                                        799*9**************************************99999*************************** PP

                         TIGR01238   76 vqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqve 150 
                                        v  a+d+a + f  wsa +  era +l++lad+ e ++ el a++ reaGkt+ + iaevreavdflr+ya+++e
  lcl|FitnessBrowser__Dino:3608920  591 VACALDAAETGFRDWSARPVSERADMLRKLADMYEDNIAELTAITTREAGKTVLDGIAEVREAVDFLRFYANEAE 665 
                                        **************************************************************************8 PP

                         TIGR01238  151 dvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpG 225 
                                           +e+  +++G +vcispwnfplaiftGqiaaal+ Gn+v+akpaeqt++iaarav+++++ G+p +++qllpG
  lcl|FitnessBrowser__Dino:3608920  666 RLEEEDPGRPRGIFVCISPWNFPLAIFTGQIAAALVMGNAVLAKPAEQTPIIAARAVQMMRDCGLPDAALQLLPG 740 
                                        88888999******************************************************************* PP

                         TIGR01238  226 rGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvadvlasafd 300 
                                         G  vG  ltsd+riaGv ftGsteva  i+kalak   ++++l+aetGG namivdstal eq v+d+l s+f+
  lcl|FitnessBrowser__Dino:3608920  741 DGPMVGGPLTSDPRIAGVCFTGSTEVAMIIHKALAKNAGPEAVLVAETGGLNAMIVDSTALHEQAVRDILISSFQ 815 
                                        *************************************************************************** PP

                         TIGR01238  301 saGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvk 375 
                                        saGqrcsalr+l+vqedv d++++++ Ga+d l++g   +l  dv pvida+a+ ++l +i++ ++ +  ++ + 
  lcl|FitnessBrowser__Dino:3608920  816 SAGQRCSALRILYVQEDVHDKLMEMLSGALDALVIGDSWNLDVDVSPVIDADAQSDILGYIDQHRKAGTLIKTLA 890 
                                        ****************************************************************99999998887 PP

                         TIGR01238  376 leddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqie 450 
                                          d      gt+v+p ++++  ++++++e+fGpvlhv  +ka+e+d+vvd ina+ yglt+G+h+ri++ v qi 
  lcl|FitnessBrowser__Dino:3608920  891 APD-----SGTYVTPAIVKVGGIADMEREIFGPVLHVATFKANEIDQVVDAINARRYGLTFGLHTRIDDRVEQIV 960 
                                        777.....8****************************************************************** PP

                         TIGR01238  451 krakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrv 498 
                                        +r++vGnvyvnrn++Ga+vG qpfGGeGlsGtGpkaGGplyl r+ +v
  lcl|FitnessBrowser__Dino:3608920  961 ERIQVGNVYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPLYLTRFRKV 1008
                                        ********************************************9886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0017
                         TIGR01238  158 akalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGa 232 
                                        + ++G+v+c+ p      i + q + al aG +v+      t+l      + l +aG p  ++    G  +    
  lcl|FitnessBrowser__Dino:3608920 1089 MVPRGTVLCLGPTP---EIAMAQAVQALGAGCAVVIALPGSTPLS-----QPLSDAGAPVVTL---DGTVD--CV 1150
                                        55688888888853...5778899999999998765555678985.....45889**998775...57777..56 PP

                         TIGR01238  233 altsderiaGviftGstevarlinkalakredapvpliae 272 
                                        +lt+ + i+ v+ +G+++ +r ++ al++r+ + +pli +
  lcl|FitnessBrowser__Dino:3608920 1151 TLTELTGIEVVAAAGASDWTRTLRVALSQRDGPIIPLIVD 1190
                                        8*******************************99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1221 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 17.94
//
[ok]

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

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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 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