GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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