GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Desulfoscipio geothermicus DSM 3669

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_092487896.1 BM299_RS18360 enoyl-CoA hydratase-related protein

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>NCBI__GCF_900115975.1:WP_092487896.1
          Length = 260

 Score =  207 bits (527), Expect = 2e-58
 Identities = 114/260 (43%), Positives = 161/260 (61%), Gaps = 2/260 (0%)

Query: 1   MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EK 59
           M + N+L+E    + ++T+NRPK LNALN   + EL AA+ +   DD +  I++TG+ EK
Sbjct: 1   MGWNNLLLEKEAGIAVLTINRPKVLNALNAETLQELDAAMDQLGNDDEVRVIILTGAGEK 60

Query: 60  AFAAGADIGMMSTYTYMDVYKGDYITRN-WETVRSIRKPIIAAVAGFALGGGCELAMMCD 118
           AF AGADI  M T   ++      + +  +  + ++ KP+IAA+ GFALGGGCEL+M CD
Sbjct: 61  AFVAGADIAFMQTLKPLEAKNFARLGQKVFSKIENLPKPVIAAINGFALGGGCELSMACD 120

Query: 119 IIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVS 178
           I  A++ AK GQPE+ LG++ G GGTQRL R V+   A ++  TA   DA  A R GLV+
Sbjct: 121 IRIASENAKLGQPEVNLGLIAGFGGTQRLTRLVNPGLAKEILFTADMYDAEAAHRIGLVN 180

Query: 179 RVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATE 238
            V+PA  L++     A  IA     AV + K++VN   E  L +    E  LF  +FATE
Sbjct: 181 HVVPAGELMNFCKNMAKRIAARGPVAVQLSKQAVNDGLEMDLEKAFVHEADLFGLVFATE 240

Query: 239 DQKEGMAAFVEKRKPVFKHR 258
           D++EG+AAF+ K+KP FK R
Sbjct: 241 DREEGIAAFLGKKKPEFKGR 260


Lambda     K      H
   0.321    0.134    0.380 

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: 172
Number of extensions: 7
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: 258
Length of database: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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