Aligments for a candidate for gabD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for gabD in Cupriavidus basilensis 4G11

Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate RR42_RS24555 RR42_RS24555 succinate-semialdehyde dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS24555
          Length = 494

 Score =  620 bits (1598), Expect = 0.0
 Identities = 304/480 (63%), Positives = 373/480 (77%)

Query: 3   LNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALP 62
           L DPSLL  + ++   W +A+   + A+TNPATG ++A V  +  AE ++AI A+  A  
Sbjct: 15  LRDPSLLETRAWLASGWQEASGGRSFAVTNPATGEILARVASLSGAEVESAITASAQAQA 74

Query: 63  AWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEE 122
            W+  ++ ER   LR WF+L+  N+DDLAL+MTSEQGKPL EA+GE+ YAASF+EWFAEE
Sbjct: 75  VWQRRSSHERAKLLRAWFDLMIANADDLALIMTSEQGKPLAEARGEILYAASFVEWFAEE 134

Query: 123 AKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPA 182
           AKRIYGD  P  Q DKRI+VI+QPVGV AAITPWNFPAAMITRK APALAAGC+++V+PA
Sbjct: 135 AKRIYGDVAPHPQTDKRILVIRQPVGVCAAITPWNFPAAMITRKVAPALAAGCSIIVRPA 194

Query: 183 PQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLM 242
             TP TALALAVLAERAGIPAGV  ++ G +  IG  +  +P+VRKLSFTGST VG  LM
Sbjct: 195 DLTPLTALALAVLAERAGIPAGVLQMVCGPSREIGAVLTASPVVRKLSFTGSTEVGRVLM 254

Query: 243 AQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVY 302
           +Q +PT+K+LSLELGGNAPFIVFDDA++DAA+EGAM +KYRN+GQTCVCANR  VQ G+Y
Sbjct: 255 SQSSPTIKRLSLELGGNAPFIVFDDADLDAAIEGAMASKYRNSGQTCVCANRFLVQDGIY 314

Query: 303 DEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHE 362
           D F E L   VA+LKVG G+  GV  GPLI  +A E +Q+ ++DA+ KGA V+ GGK H 
Sbjct: 315 DRFVEALVRRVAELKVGNGVEPGVQQGPLIQKSACEHLQAMIDDAVGKGAKVVVGGKGHA 374

Query: 363 LGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRD 422
           LGG FFEPTV+  A   MRVAREE FGP+AP+F+F D  + I  ANDTE+GLAAY Y RD
Sbjct: 375 LGGTFFEPTVIAGATPDMRVAREELFGPVAPVFRFRDEAEAIALANDTEYGLAAYLYTRD 434

Query: 423 ISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICMSV 482
            + +W+V E+LEYGMVG+NTGLIS EVAPFGG+K SGLGREGS+YGI+EYLEIKY+C  V
Sbjct: 435 NARIWRVGEALEYGMVGLNTGLISNEVAPFGGVKQSGLGREGSRYGIDEYLEIKYLCAQV 494


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: 702
Number of extensions: 22
Number of successful extensions: 1
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: 494
Length adjustment: 34
Effective length of query: 448
Effective length of database: 460
Effective search space:   206080
Effective search space used:   206080
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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, 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