Alignments for a candidate for gabD in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabD in Shewanella loihica PV-4

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__PV4:5208455
          Length = 498

 Score =  575 bits (1481), Expect = e-168
 Identities = 277/489 (56%), Positives = 366/489 (74%), Gaps = 4/489 (0%)

Query: 9   WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68
           WQ+ A SL I+ + FINGEY AA  N+TF+ + P+    L ++A    +D +RA++ AR 
Sbjct: 10  WQEMADSLVIQGQAFINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANARE 69

Query: 69  VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128
           VFERGDWS   P KRK V+ + ADL+EA+ +ELALLETLD GKPIR+S   D+ GAARA+
Sbjct: 70  VFERGDWSQLPPVKRKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARAL 129

Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188
           RW  EA+DK+Y E+A T+ +E+ MI REPVGV+AAIVPWNFPLL+ CWKLGPALA GNSV
Sbjct: 130 RWSGEAVDKIYDEIAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSV 189

Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248
           +LKPSEKSPL+AIR+A LA EAG+P GVLNV+ G+GH  G+AL+ H D+D + FTGST+ 
Sbjct: 190 VLKPSEKSPLTAIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKI 249

Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308
            KQL+  AG+SNMKRVWLEAGGKS NIVF D P+L++AA A A+ I +NQG+VC AG+RL
Sbjct: 250 AKQLMIYAGESNMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRL 309

Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368
           L+E  + +E + L++ + Q WQPGHPLDPATT G ++D    ++V  +IR G ++G  L 
Sbjct: 310 LVESGVKEELINLIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLR 369

Query: 369 DGRNAGLAAA----IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424
            G    LA      + PTIF +V    ++++EEIFGPVL V  F   E+A+++ ND+ YG
Sbjct: 370 QGGQQVLAETGGVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYG 429

Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFT 484
           L A VWT D+S+AH+ ++ L++G V++N+Y+ GDMT PFGGYKQSGNGRDKSLHA +K+T
Sbjct: 430 LAAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFDKYT 489

Query: 485 ELKTIWISL 493
           E+K  WI+L
Sbjct: 490 EIKATWIAL 498


Lambda     K      H
   0.317    0.133    0.389 

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: 664
Number of extensions: 18
Number of successful extensions: 2
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: 495
Length of database: 498
Length adjustment: 34
Effective length of query: 461
Effective length of database: 464
Effective search space:   213904
Effective search space used:   213904
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: 52 (24.6 bits)

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

Downloads

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

Related tools

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, or view the source code.

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