GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>MicrobesOnline__882:209027
          Length = 368

 Score =  217 bits (553), Expect = 3e-61
 Identities = 132/353 (37%), Positives = 199/353 (56%), Gaps = 16/353 (4%)

Query: 4   VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63
           + +R ++ NF     LD ++L+I +GEFL LLG SGCGK+T+L  I+G      G I +K
Sbjct: 8   IELRGVTKNFEDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLK 67

Query: 64  DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123
            + +    P+ R +  VFQ+YAL+P M+V +N+ FGL++ + P  EI +RV  A  ++ +
Sbjct: 68  GQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHL 127

Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183
           +    R+P +LSGGQ+QRVAI RA+V +  V L DEP S LD KLR ++++EIK L + L
Sbjct: 128 EAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQL 187

Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFR 243
             T ++VTHDQ EA  ++DR+ VM  G I+Q+  P  IY  P NL+VA F+G   +N   
Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVG--EINILN 245

Query: 244 GEVEPKDGRSFVRA--GGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQ 301
             +    G     A   G+ F +    +     PG KV + LRPE ++V    +  P   
Sbjct: 246 AVIAANHGDGLYDAVIEGVTFPIR---SQRTFAPGDKVNVLLRPEDLRVYTLTEDRPAGP 302

Query: 302 AVVD-IEEPM--GA--DNLLWLTFAGQSMSVRIAGQR----RYPPGSTVRLSF 345
            +   IEE +  GA  D ++ L+   + M+     +      Y PG TV +S+
Sbjct: 303 HLTGRIEESVYKGATVDLIVTLSDGRRLMAAEFFNEDDVDINYNPGETVTVSW 355


Lambda     K      H
   0.320    0.137    0.392 

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: 338
Number of extensions: 11
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: 361
Length of database: 368
Length adjustment: 29
Effective length of query: 332
Effective length of database: 339
Effective search space:   112548
Effective search space used:   112548
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: 49 (23.5 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