GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamI in Synechococcus elongatus PCC 7942

Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate Synpcc7942_2557 Synpcc7942_2557 bidirectional hydrogenase complex protein HoxU

Query= uniprot:Q39TW6
         (218 letters)



>FitnessBrowser__SynE:Synpcc7942_2557
          Length = 238

 Score =  107 bits (266), Expect = 2e-28
 Identities = 72/209 (34%), Positives = 99/209 (47%), Gaps = 30/209 (14%)

Query: 1   MSEINLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVEVRGWP 60
           MS + LQID +E+ A  G T+L  A+   I IPTLCH + +   G CR+C   VEV G P
Sbjct: 1   MSVVTLQIDDQELAANVGQTVLQVAREASIPIPTLCHLQGVSDVGACRLCV--VEVAGSP 58

Query: 61  KLVAGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAH---------APDSEELKALAQEY 111
           KL   C+  V +GLVV+TR+ ++++ R+ ++E   A          A  + EL+  A   
Sbjct: 59  KLQPACLLTVSEGLVVQTRSPRLERYRRQIVELFFAEGNHVCAICVANGNCELQDAAIAV 118

Query: 112 GADRDRFE----------KHPSF------CIHCGLCVRYCAEIKKKNAVGFVDRGSNREI 155
           G D  R+            H  F      CI C  CVR C EI+  +      RG +  I
Sbjct: 119 GMDHSRYPYRFPKRDVDLSHRFFGLDHNRCILCTRCVRVCDEIEGAHVWDVAMRGEHCRI 178

Query: 156 ---SFIPEIAAKECWDCKECFPLCPTSAL 181
                 P  A   C +C +C   CPT AL
Sbjct: 179 VAGMDQPWGAVDACTNCGKCIDACPTGAL 207


Lambda     K      H
   0.320    0.137    0.432 

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: 169
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: 218
Length of database: 238
Length adjustment: 23
Effective length of query: 195
Effective length of database: 215
Effective search space:    41925
Effective search space used:    41925
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 (21.8 bits)
S2: 46 (22.3 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