Alignments for a candidate for putA in Sphingomonas indica Dd16

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Sphingomonas indica Dd16

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_085217646.1 B9N75_RS04120 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::psRCH2:GFF3021
         (1053 letters)



>NCBI__GCF_900177405.1:WP_085217646.1
          Length = 999

 Score =  875 bits (2260), Expect = 0.0
 Identities = 495/1030 (48%), Positives = 645/1030 (62%), Gaps = 54/1030 (5%)

Query: 28   YSVDEAQYLTELLQLADPGEAGIAAIRERARSLIEAVRGRDNAVDTLDALLRQYSLDTQE 87
            Y + E + L  LL+ A         +  RA  ++  +R   +    ++  L++Y L+T E
Sbjct: 16   YRLPEPEVLAPLLKDAALDPDSRRRVEHRALGMLAELRAAQST-GWVNQFLQEYRLNTSE 74

Query: 88   GLMLMCLAEALLRVPDAATADALIRDKLNAAEWERHLGQSDNVLVNFAAWGLVMTGKVVD 147
            G+ L+ LAEA LRVPD  TAD LI DKL   +W  H G+S + LVN A WGLV+   +V 
Sbjct: 75   GVALLSLAEAFLRVPDPETADDLIADKLGDGDWRAHTGRSHSGLVNSATWGLVIGRALV- 133

Query: 148  PETADGRPKNVIGRLLKRSGEPVIRGAMNQAMKLMGKQFVLGRTISEALKNGRPEREKGY 207
               ++    + + RLL R+GEP +R  +  AM+LMG+ FV+GRTI EA+        +G+
Sbjct: 134  ---SESEQASALKRLLSRAGEPFVRQGVGAAMRLMGEIFVMGRTIDEAIGRMGKRDNRGF 190

Query: 208  TYSFDMLGEAALTAEDAAKYMADYRQAVETVGAEPQVGKGPRPSVSIKLSALHPRYELAQ 267
            T SFDMLGEAA T  DA +Y A Y  A+  VG   + G     S+S+KLSAL+PRYE+ Q
Sbjct: 191  TASFDMLGEAARTTPDAERYFAAYENAIRAVGRVSEQGH----SISVKLSALYPRYEVTQ 246

Query: 268  RERVLTELFGSVRELAILARRLNVGITIDAEEADRLELSLELYEKLLRDPAIAGWGEFGL 327
             +R +  L   V  LA LA  + + +TIDAEE++RLE+SL++ E + + PA+ GW   G+
Sbjct: 247  YDRCVPSLIEQVEALATLAAHVGIPLTIDAEESERLEMSLDIIEAVAKLPALKGWDGLGM 306

Query: 328  VIQAYSKRCLPVLVWLTLLGRELGERIPLRLVKGAYWDSEIKQCQVQGLDGYPVYTRKEG 387
             +QAY KR  P + W   +    G  + +RLVKGAYWDSEIK+ Q  GL  YP++TRK  
Sbjct: 307  AVQAYGKRARPTIAWADAVAAATGRTMAVRLVKGAYWDSEIKRNQEGGLTDYPLFTRKAA 366

Query: 388  TDTSYLACARYLLSEHTRGVIYPQFASHNAHTVSCILAMAEETAQPREFEFQRLHGMGDA 447
            TD SYLACA+ +L+      I P FA+HNA TV+ IL  A      R+FEFQRLHGMG+ 
Sbjct: 367  TDVSYLACAKDMLAAK---YIRPAFATHNALTVATILEWA---GAARDFEFQRLHGMGEG 420

Query: 448  LYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRLLENGANSSFVHQLVDPRVPVESLIDHP 507
            LY+T++       RIYAPVG H+DLL YLVRRLLENGANSSFVHQL D  +    L+  P
Sbjct: 421  LYETLVRDQGYATRIYAPVGGHRDLLAYLVRRLLENGANSSFVHQLADTTLTDVDLLTDP 480

Query: 508  VTQLRRFAAPGNPRIPLPPALF-GNRKNSQGINMNIQNQWTELASAYQ---PFLERQWQA 563
            V ++ R     +P IPLP  LF   RKNS+G++++   +   + +A     PFL+++   
Sbjct: 481  VDKIARVGGTRHPSIPLPEDLFMPERKNSRGLDLSDDTELARVKAAVNAPLPFLDKK--- 537

Query: 564  APVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQARQAIDRLAAYWPIWNATPVEARA 623
            AP                           +   A +A+ A+      +P W+   VE RA
Sbjct: 538  AP--------------------------PKGDDASRAQSAVATALRGFPAWSRRSVEDRA 571

Query: 624  AVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVREAVDFCRYYAQQARLKLGREELK 683
            A L+RL DLLE+ R  LMAL   EA K++ D + EVREAVDFCRYYA QAR +L   EL 
Sbjct: 572  ACLDRLADLLERERDTLMALAVQEAFKTIPDALAEVREAVDFCRYYAAQARSRLQPIELP 631

Query: 684  GPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAALVAGNTVLAKPAEQTSLIAARAL 743
            GPTGERN L   GRG FVC++PWNFPLAI+LGQ++AALVAGNTV+AKPA QT  IAA A+
Sbjct: 632  GPTGERNVLRMGGRGAFVCIAPWNFPLAIFLGQVSAALVAGNTVIAKPAPQTPEIAAFAV 691

Query: 744  ELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVCFTGSTDTARIINRQL-AEKEGPI 802
             L   AG+P++A+ +  G G  +G     DPRV GV FTGST TA+ I R L A+   PI
Sbjct: 692  GLAHGAGIPEDALVYAAG-GPDMGAALVADPRVAGVAFTGSTATAKRIARSLVADDARPI 750

Query: 803  ATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQRCSALRVLYVQRDIADRVIDLL 862
              LIAETGG NAMIVDSTALPEQV+ D V S+F SAGQRCSALR+L +Q +IADR +++L
Sbjct: 751  VPLIAETGGINAMIVDSTALPEQVVADVVTSSFRSAGQRCSALRLLVLQEEIADRTLEML 810

Query: 863  KGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQLKSEGRLIAEATVPAGLNGHFVA 922
             GAM  L VG       D+GPVIDQ A + L+ H  +   E R +    VPA   G FV 
Sbjct: 811  SGAMDTLVVGDPGDPRTDVGPVIDQSAYDRLMGH--RAAMESRWLKTLPVPA--QGLFVP 866

Query: 923  PVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAINGTGYGLTLGVHSRNEETAERI 982
            P    ++ I  +++E FGP+LHV  + +  L + +  +N +GYGLT+G+HSR    A+ I
Sbjct: 867  PTLIGVERIEDVQQEWFGPLLHVTTWKSGKLAETIERVNASGYGLTMGLHSRIARAADTI 926

Query: 983  EQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAGGPSYLLRFANERTTSTNTTAVG 1042
            E L   GNLYVNR+ IGA+VG QPFGG  LSGTGPKAGGP+YL RF  ER TST+TT+ G
Sbjct: 927  EDLGEAGNLYVNRSMIGAIVGSQPFGGEGLSGTGPKAGGPNYLPRFCAERVTSTDTTSAG 986

Query: 1043 GNASLLSLGD 1052
            GNA+LLSL D
Sbjct: 987  GNATLLSLED 996


Lambda     K      H
   0.319    0.136    0.396 

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: 2496
Number of extensions: 105
Number of successful extensions: 9
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: 1053
Length of database: 999
Length adjustment: 45
Effective length of query: 1008
Effective length of database: 954
Effective search space:   961632
Effective search space used:   961632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)

Align candidate WP_085217646.1 B9N75_RS04120 (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.640513.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.6e-173  561.7   0.0   3.2e-171  556.1   0.1    2.1  2  NCBI__GCF_900177405.1:WP_085217646.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217646.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   0.0    0.0011    0.0011       1      30 [.     500     529 ..     500     538 .. 0.90
   2 !  556.1   0.1  3.2e-171  3.2e-171      72     496 ..     544     973 ..     540     977 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0011
                             TIGR01238   1 dlygegrknslGvdlaneselksleeqllk 30 
                                           dl+   rkns G+dl+ ++el+++++ +++
  NCBI__GCF_900177405.1:WP_085217646.1 500 DLFMPERKNSRGLDLSDDTELARVKAAVNA 529
                                           688889*****************9999876 PP

  == domain 2  score: 556.1 bits;  conditional E-value: 3.2e-171
                             TIGR01238  72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflry 144
                                           da+++q av +a++ f+ ws    ++raa+l+rladlle++  +l+al+v+ea kt+ +a+aevreavdf+ry
  NCBI__GCF_900177405.1:WP_085217646.1 544 DASRAQSAVATALRGFPAWSRRSVEDRAACLDRLADLLERERDTLMALAVQEAFKTIPDALAEVREAVDFCRY 616
                                           56789******************************************************************** PP

                             TIGR01238 145 yakqvedvldeesaka............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaar 205
                                           ya q++  l+                  +Ga+vci+pwnfplaif+Gq++aal+aGntviakpa qt+ iaa 
  NCBI__GCF_900177405.1:WP_085217646.1 617 YAAQARSRLQPIELPGptgernvlrmggRGAFVCIAPWNFPLAIFLGQVSAALVAGNTVIAKPAPQTPEIAAF 689
                                           ********99875444789999*************************************************** PP

                             TIGR01238 206 avellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap.vpliaetGGqn 277
                                           av l + aG+p  ++    G G d+Gaal +d+r+aGv+ftGst++a++i ++l   ++ p vpliaetGG n
  NCBI__GCF_900177405.1:WP_085217646.1 690 AVGLAHGAGIPEDALVYAAG-GPDMGAALVADPRVAGVAFTGSTATAKRIARSLVADDARPiVPLIAETGGIN 761
                                           **************988887.666*****************************9988888879********** PP

                             TIGR01238 278 amivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvid 350
                                           amivdstal+eqvvadv++s+f saGqrcsalr+l++qe++adr+l+++ Gamd l+vg p+  +tdvGpvid
  NCBI__GCF_900177405.1:WP_085217646.1 762 AMIVDSTALPEQVVADVVTSSFRSAGQRCSALRLLVLQEEIADRTLEMLSGAMDTLVVGDPGDPRTDVGPVID 834
                                           ************************************************************************* PP

                             TIGR01238 351 aeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkv 423
                                           + a ++l+ h  +m+++  k   +   +     +g fv+ptl+ ++ ++++++e fGp+lhv  +k+ +l++ 
  NCBI__GCF_900177405.1:WP_085217646.1 835 QSAYDRLMGHRAAMESRWLK--TLPVPA-----QGLFVPPTLIGVERIEDVQQEWFGPLLHVTTWKSGKLAET 900
                                           **************876544..444444.....79************************************** PP

                             TIGR01238 424 vdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrlt 496
                                           ++++na+Gyglt+G+hsri  +   ie+  ++Gn+yvnr ++Ga+vG qpfGGeGlsGtGpkaGGp yl r+ 
  NCBI__GCF_900177405.1:WP_085217646.1 901 IERVNASGYGLTMGLHSRIARAADTIEDLGEAGNLYVNRSMIGAIVGSQPFGGEGLSGTGPKAGGPNYLPRFC 973
                                           *********************************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (999 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 34.32
//
[ok]

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

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Protein sequences (fasta format)
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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