Aligments for a candidate for gabD in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for gabD in Phaeobacter inhibens BS107

Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD

Query= reanno::MR1:200453
         (482 letters)



>lcl|FitnessBrowser__Phaeo:GFF2918 PGA1_c29650
           succinate-semialdehyde dehdyrogenase GabD
          Length = 491

 Score =  617 bits (1592), Expect = 0.0
 Identities = 311/482 (64%), Positives = 376/482 (78%), Gaps = 2/482 (0%)

Query: 2   LLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAAL 61
           LL DPSLL  + YI G + D  +  T A+ NPA G VIA V  + +++   AIA AE A 
Sbjct: 11  LLTDPSLLEPRAYIGGAFVDG-ADGTFAVKNPARGDVIANVADVSRSQVAGAIAQAEVAQ 69

Query: 62  PAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAE 121
             W   T KER   LR+WF+L+ EN +DLA+++T+E GKPL E++GE+ Y ASFIE+FAE
Sbjct: 70  KDWAKWTGKERANVLRKWFDLMMENQEDLAVILTAEMGKPLAESRGEIGYGASFIEFFAE 129

Query: 122 EAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKP 181
           EAKRIYG+TIPGHQ DKRI V+KQP+GV A+ITPWNFP AMITRKA PALAAGC  V +P
Sbjct: 130 EAKRIYGETIPGHQRDKRITVLKQPIGVAASITPWNFPNAMITRKAGPALAAGCAFVARP 189

Query: 182 APQTPFTALALAVLAERAGIPAGVFSVITG-DAIAIGNEMCTNPIVRKLSFTGSTNVGIK 240
           A  TP +A ALAVLA+RAGIPAGVF+V+T  +A   G E C N  VRKL+FTGST VG  
Sbjct: 190 AELTPLSATALAVLADRAGIPAGVFNVVTSSNASETGKEFCENNAVRKLTFTGSTEVGRI 249

Query: 241 LMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300
           LM Q A T+ K S+ELGGNAPFIVFDDA++DAAVEGA++ K+RN GQTCVCANRIYVQAG
Sbjct: 250 LMRQAADTVMKCSMELGGNAPFIVFDDADLDAAVEGAIMCKFRNNGQTCVCANRIYVQAG 309

Query: 301 VYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKV 360
           VYD FA KL  AVAK+ VG+G+  G   GPLIN  AVEKVQ+H+ DA +KGA V+ GG  
Sbjct: 310 VYDAFAAKLKEAVAKMTVGDGLAEGTQFGPLINEKAVEKVQAHIADAKEKGAEVILGGNP 369

Query: 361 HELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYG 420
            ELGG FFEPT++T A + M  +++ETFGP+APLFKF   DDVI+ ANDT FGLA+YFY 
Sbjct: 370 SELGGTFFEPTIITGATQDMVFSQDETFGPMAPLFKFETEDDVIEMANDTIFGLASYFYA 429

Query: 421 RDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICM 480
           +D+S V+KVAE+LEYG+VGVNTG+ISTE+APFGG+K SGLGREGS +GIE+YLE+KYICM
Sbjct: 430 KDLSRVYKVAEALEYGIVGVNTGIISTELAPFGGVKQSGLGREGSHHGIEDYLEMKYICM 489

Query: 481 SV 482
           SV
Sbjct: 490 SV 491


Lambda     K      H
   0.318    0.133    0.390 

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: 674
Number of extensions: 19
Number of successful extensions: 3
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: 482
Length of database: 491
Length adjustment: 34
Effective length of query: 448
Effective length of database: 457
Effective search space:   204736
Effective search space used:   204736
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.

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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, 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