GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate H281DRAFT_06394 H281DRAFT_06394 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__Burk376:H281DRAFT_06394
          Length = 233

 Score =  191 bits (485), Expect = 1e-53
 Identities = 100/234 (42%), Positives = 150/234 (64%), Gaps = 5/234 (2%)

Query: 8   VLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIE 67
           ++L V+ +   YG    ++GV  ++ EGE V+L+G NGAGK+TT+KAI G ++  +G++ 
Sbjct: 1   MILDVQQIHGFYGKSHILQGVSLQIAEGETVTLLGRNGAGKSTTLKAIAGVVAPKNGSVT 60

Query: 68  YLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFT 127
           + G +I G     +   G+  VPE RG+F  +T+ ENL++GA  RKD    L DI   + 
Sbjct: 61  FNGATISGLQPHKIASRGVCFVPEHRGIFRLLTVEENLRLGA--RKDSPWQLDDI---YR 115

Query: 128 IFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRD 187
           IFPRL+ER+    G +SGGEQQMLA+GRALM+ P++L+LDEP  GL+P++V++I   ++ 
Sbjct: 116 IFPRLKERRTNGGGQLSGGEQQMLAVGRALMNHPRLLMLDEPVEGLAPVIVEEIVAQLKL 175

Query: 188 VYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
           +   GV I+LVEQN      +ADR Y++E G+I  +G       D  V+  YLG
Sbjct: 176 IREAGVAILLVEQNLEVCTQLADRHYIIEQGVIVYSGDNASFAADDSVKDRYLG 229


Lambda     K      H
   0.317    0.136    0.373 

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: 192
Number of extensions: 5
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: 242
Length of database: 233
Length adjustment: 23
Effective length of query: 219
Effective length of database: 210
Effective search space:    45990
Effective search space used:    45990
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: 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