Alignments for a candidate for gnd in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Shewanella amazonensis SB2B

Align 6-phosphogluconate dehydrogenase, decarboxylating; EC 1.1.1.44 (characterized)
to candidate 6937195 Sama_1365 6-phosphogluconate dehydrogenase (RefSeq)

Query= SwissProt::P85968
         (483 letters)



>FitnessBrowser__SB2B:6937195
          Length = 511

 Score =  432 bits (1111), Expect = e-125
 Identities = 236/497 (47%), Positives = 316/497 (63%), Gaps = 34/497 (6%)

Query: 5   DIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVD--------DFLAKEA--KGTKVIG 54
           DI +IGL VMG+NL LN+ D+G+ V AF+   +KV         +  AK A  K T++ G
Sbjct: 9   DIGVIGLGVMGKNLALNIADNGYRVAAFDLDGAKVRAAVSQSQAEVAAKPAHSKATQLTG 68

Query: 55  AKSLKDMVSKLKKPRRVILLVKAGQAVDDFIEKLVPL-LDTGDIIIDGGNSEYRDTTRRC 113
             SLK M+  L  PR ++L V AG  VD     L+   +   DI+ID GNS + DT +R 
Sbjct: 69  VDSLKSMLCALTSPRLLLLSVPAGAPVDGVCSALIDAGIKPDDIVIDTGNSLWTDTVKRE 128

Query: 114 QDLKAKGILFVGSGVSGGEEGARYGPSLMPGGNKEAWPHIKTIFQAIAAKVGT------- 166
           Q+   K + F  S VSGGE GAR+GPSLMP G KEAW  +  I++AIAAKV         
Sbjct: 129 QEYAGKFVFF-SSAVSGGEVGARFGPSLMPSGKKEAWDSVAPIWRAIAAKVDNTTGLPIE 187

Query: 167 ----------GEPCCDWVGDEGAGHFVKMVHNGIEYGDMQLICEAYHLMKDVLGMRHEEM 216
                     GEPC  ++G  G+GH+VKMVHNGIEY DMQLICEAY L+ DVLG+   E+
Sbjct: 188 RFEPGNPVLEGEPCTAYIGPAGSGHYVKMVHNGIEYADMQLICEAYQLLSDVLGLSAVEI 247

Query: 217 AQAFEDWNKTELDSFLIEITANILKFQDT-DGKELLPKIRDSAGQKGTGKWTAISALEYG 275
           A  FE WN+ +L+S+L+ I+A +L+  D   GK L+  I D AGQKGTG WTA+S+L+ G
Sbjct: 248 AAIFERWNRGKLNSYLMGISAEVLRQSDPLTGKPLVEMILDKAGQKGTGLWTAVSSLQIG 307

Query: 276 MPVTLIGEAVFARCLSSLKEERVQASRKLKGPKMVQLEG-SKQAFLEDVRKALYASKIIS 334
            P   I EAV+AR LS+ K  R + + +L G   + L+G    +F++++ +AL+ +KI  
Sbjct: 308 TPAPTIAEAVYARALSNQKALRTELAGRLAGA--MPLQGIDATSFIDELEQALFCAKICC 365

Query: 335 YAQGFMLLRQAATEFGWTLNYGGIALMWRGGCIIRSVFLGKIKDAFERNPELQNLLLDDF 394
           YAQGF L+   A E GW L++  IA +WR GCIIR+ FL  I DAFE  P+L NLL+   
Sbjct: 366 YAQGFQLMAMNAAEQGWELDFAAIARIWRAGCIIRATFLQSITDAFEAEPKLANLLIAKS 425

Query: 395 FKSAVDDCQDSWRRVISTGVQAGIPMPCFTTALSFYDGYRHEMLPANLIQAQRDYFGAHT 454
           F  A+ + Q SWR ++S  V AG+P PC T+AL++YDGYR E LPANL+Q QRDYFGAH+
Sbjct: 426 FAEALSEAQQSWRHLVSKAVLAGVPAPCITSALAYYDGYRRETLPANLLQGQRDYFGAHS 485

Query: 455 YELL-SKPGEFIHTNWT 470
           +E + ++ GE  H NW+
Sbjct: 486 FERIDTQAGEKYHLNWS 502


Lambda     K      H
   0.320    0.137    0.414 

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: 620
Number of extensions: 33
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: 483
Length of database: 511
Length adjustment: 34
Effective length of query: 449
Effective length of database: 477
Effective search space:   214173
Effective search space used:   214173
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: 52 (24.6 bits)

Align candidate 6937195 Sama_1365 (6-phosphogluconate dehydrogenase (RefSeq))
to HMM TIGR00873 (gnd: 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44))

# 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/TIGR00873.hmm
# target sequence database:        /tmp/gapView.20950.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00873  [M=467]
Accession:   TIGR00873
Description: gnd: 6-phosphogluconate dehydrogenase (decarboxylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.3e-178  580.5   0.0   1.3e-133  432.1   0.0    2.0  2  lcl|FitnessBrowser__SB2B:6937195  Sama_1365 6-phosphogluconate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937195  Sama_1365 6-phosphogluconate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   0.0   5.4e-47   5.4e-47       1     163 [.       9     181 ..       9     186 .. 0.89
   2 !  432.1   0.0  1.3e-133  1.3e-133     161     466 ..     197     502 ..     189     503 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 5.4e-47
                         TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellke..........eakgkklvgaesieefvkslekPrki 67 
                                       diG+iGl+vmGknl+lniad+G+ va+++ + +k+++ + +          ++k ++l+g+ s+++++ +l  Pr +
  lcl|FitnessBrowser__SB2B:6937195   9 DIGVIGLGVMGKNLALNIADNGYRVAAFDLDGAKVRAAVSQsqaevaakpaHSKATQLTGVDSLKSMLCALTSPRLL 85 
                                       79****************************99999887765222222222234567899****************** PP

                         TIGR00873  68 lllvkaGaavdavieellpl.lekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGsk 143
                                       ll v aGa+vd v ++l+++ +++ di+id Gnsl++dt +re+e + k + f  + vsGGe Gar+GPslmp G+k
  lcl|FitnessBrowser__SB2B:6937195  86 LLSVPAGAPVDGVCSALIDAgIKPDDIVIDTGNSLWTDTVKREQEYAGK-FVFFSSAVSGGEVGARFGPSLMPSGKK 161
                                       ****************99865999*********************9876.678899********************* PP

                         TIGR00873 144 eayelvepilqkiaakvege 163
                                       ea+++v+pi ++iaakv+++
  lcl|FitnessBrowser__SB2B:6937195 162 EAWDSVAPIWRAIAAKVDNT 181
                                       *****************986 PP

  == domain 2  score: 432.1 bits;  conditional E-value: 1.3e-133
                         TIGR00873 161 egepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeiaevfeeWnegeldsylieitadilkk 237
                                       egepc+ yiG++G+GhyvkmvhnGiey+dmqli+eay+ll ++l+lsa eia++fe+Wn+g+l+syl+ i+a++l++
  lcl|FitnessBrowser__SB2B:6937195 197 EGEPCTAYIGPAGSGHYVKMVHNGIEYADMQLICEAYQLLSDVLGLSAVEIAAIFERWNRGKLNSYLMGISAEVLRQ 273
                                       79*************************************************************************** PP

                         TIGR00873 238 kded.GkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfarvlsslkeervaaskllsgplaeekaedkee 313
                                        d   Gkplv++ild+agqkGtG Wta+++l+ G+P  +i+e+v+ar+ls +k  r++ +  l+g +  +   d+ +
  lcl|FitnessBrowser__SB2B:6937195 274 SDPLtGKPLVEMILDKAGQKGTGLWTAVSSLQIGTPAPTIAEAVYARALSNQKALRTELAGRLAGAMPLQG-IDATS 349
                                       **977***********************************************************9887776.6**** PP

                         TIGR00873 314 fiedvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrgGciirskfldkikkafeenpelenlllaeyf 390
                                       fi+++++al+++ki++yaqGf+l+++ ++e gw+l++++ia+iwr+Gciir++fl++i++afe++p+l+nll+a+ f
  lcl|FitnessBrowser__SB2B:6937195 350 FIDELEQALFCAKICCYAQGFQLMAMNAAEQGWELDFAAIARIWRAGCIIRATFLQSITDAFEAEPKLANLLIAKSF 426
                                       ***************************************************************************** PP

                         TIGR00873 391 kdalkkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeffhteWl 466
                                       ++al++aq+++r+ v+ka+ +g+p P++++al++ydgyr+++lpanllq+qrdyfGah++er+d++ ge++h +W+
  lcl|FitnessBrowser__SB2B:6937195 427 AEALSEAQQSWRHLVSKAVLAGVPAPCITSALAYYDGYRRETLPANLLQGQRDYFGAHSFERIDTQAGEKYHLNWS 502
                                       ***************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (511 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: 00:00:00.02
# Mc/sec: 10.91
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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SQLite3 databases

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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