Alignments for a candidate for gabD in Williamsia sterculiae CPCC 203464

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabD in Williamsia sterculiae CPCC 203464

Align Putative succinate-semialdehyde dehydrogenase [NADP(+)] 2; SSADH 2; SSDH 2; EC 1.2.1.79 (characterized)
to candidate WP_076482557.1 BW971_RS18565 succinate-semialdehyde dehydrogenase (NADP(+))

Query= SwissProt::P9WNX7
         (518 letters)



>NCBI__GCF_900156495.1:WP_076482557.1
          Length = 517

 Score =  626 bits (1614), Expect = 0.0
 Identities = 316/517 (61%), Positives = 386/517 (74%)

Query: 1   MPAPSAEVFDRLRNLAAIKDVAARPTRTIDEVFTGKPLTTIPVGTAADVEAAFAEARAAQ 60
           M  P++  FDRLR L+AI D   R  R + E FTG P+  IPVGTA DV AA   AR AQ
Sbjct: 1   MSRPTSATFDRLRALSAIDDPDTREQRDVLEAFTGTPMARIPVGTADDVRAAVDRAREAQ 60

Query: 61  TDWAKRPVIERAAVIRRYRDLVIENREFLMDLLQAEAGKARWAAQEEIVDLIANANYYAR 120
             WA     ER+AVI R+ DLV E R+ LMD  QAE GKAR  AQEE+VD+   A +YA+
Sbjct: 61  RAWADTWPKERSAVIARFADLVFEYRDALMDFAQAETGKARAYAQEEVVDVALTARHYAK 120

Query: 121 VCVDLLKPRKAQPLLPGIGKTTVCYQPKGVVGVISPWNYPMTLTVSDSVPALVAGNAVVL 180
           V   LL  ++A+ ++PG     + YQPKGVVGVISPWNYP+TL  SD+V AL+AGNAVV+
Sbjct: 121 VAPGLLAAKRAKGMIPGATDVRIRYQPKGVVGVISPWNYPLTLAASDAVAALMAGNAVVI 180

Query: 181 KPDSQTPYCALACAELLYRAGLPRALYAIVPGPGSVVGTAITDNCDYLMFTGSSATGSRL 240
           KPDSQTPYCALA A+LLYRAGLPR L+A+VPG G VVG  + +  DYLMFTGS+ATGS L
Sbjct: 181 KPDSQTPYCALAVADLLYRAGLPRELFAVVPGSGGVVGRELVEQVDYLMFTGSTATGSLL 240

Query: 241 AEHAGRRLIGFSAELGGKNPMIVARGANLDKVAKAATRACFSNAGQLCISIERIYVEKDI 300
           AE AGRRLIGFSAELGGKN MIV   A++D   + A RAC+SN+GQLCISIER+YVE+ +
Sbjct: 241 AEQAGRRLIGFSAELGGKNAMIVTADADVDNAVEGAVRACYSNSGQLCISIERLYVERPV 300

Query: 301 AEEFTRKFGDAVRNMKLGTAYDFSVDMGSLISEAQLKTVSGHVDDATAKGAKVIAGGKAR 360
           A+EFTR+F   V  M++G  YDF+ +MGSL S+AQ+  V+ HV+DA AKGA V+AGG+ R
Sbjct: 301 ADEFTRRFAARVERMEVGADYDFAAEMGSLASQAQVDAVTAHVEDAKAKGATVLAGGRPR 360

Query: 361 PDIGPLFYEPTVLTNVAPEMECAANETFGPVVSIYPVADVDEAVEKANDTDYGLNASVWA 420
           PD+GP FY PTVL+ V   MEC  +ETFGP+VSIYPV  VDEA+E ANDT YGLNA+V+A
Sbjct: 361 PDLGPFFYSPTVLSGVDEAMECFGSETFGPLVSIYPVDSVDEAIELANDTTYGLNAAVFA 420

Query: 421 GSTAEGQRIAARLRSGTVNVDEGYAFAWGSLSAPMGGMGLSGVGRRHGPEGLLKYTESQT 480
           G  AEG+RIAARL  GTVN++EGYA AWGS +APMGGMG SGVGRRHG EGLLKYTE QT
Sbjct: 421 GDPAEGRRIAARLHVGTVNLNEGYAAAWGSTAAPMGGMGASGVGRRHGDEGLLKYTEPQT 480

Query: 481 IATARVFNLDPPFGIPATVWQKSLLPIVRTVMKLPGR 517
           IAT RV  +    G+P +V+ +++   ++ +  +PGR
Sbjct: 481 IATQRVIGIGGIKGVPRSVFLRTVPTAMKALKYVPGR 517


Lambda     K      H
   0.318    0.134    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: 786
Number of extensions: 24
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: 518
Length of database: 517
Length adjustment: 35
Effective length of query: 483
Effective length of database: 482
Effective search space:   232806
Effective search space used:   232806
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 24 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 2024 update 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