GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Klebsiella michiganensis M5al

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BWI76_RS07275 BWI76_RS07275 ABC transporter

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__Koxy:BWI76_RS07275
          Length = 368

 Score =  433 bits (1113), Expect = e-126
 Identities = 216/341 (63%), Positives = 268/341 (78%), Gaps = 3/341 (0%)

Query: 14  ALLVLPLILQSFG-NAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFA 72
           ALLV P++    G N WVR+ D ALLYV+LALGLNIVVGY GLLD+G++AFYAVGAYL A
Sbjct: 25  ALLVAPMVASQLGGNYWVRVIDFALLYVMLALGLNIVVGYTGLLDMGFIAFYAVGAYLAA 84

Query: 73  LMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVT 132
           L+ASPHL D F    + FP+GLHTS  ++IP+AAL+AA  G +LGAPTLKLRGDYLAIVT
Sbjct: 85  LLASPHLLDVFPILNSWFPDGLHTSWLVIIPLAALVAAGCGIVLGAPTLKLRGDYLAIVT 144

Query: 133 LGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYL 192
           LGFGEIIRI + NLD PVN+TNG KG+  +DS+ +FGL        FGF + ++ L+YYL
Sbjct: 145 LGFGEIIRILMRNLDRPVNITNGAKGISGVDSLNLFGLKFSGVYHWFGFKVPALWLWYYL 204

Query: 193 FLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSG 252
            ++++V  + +C RLQ SRIGRAW AIREDE  A+AMGIN RN KLLAF +GASFGGV+G
Sbjct: 205 LMLVIVAIIFVCLRLQHSRIGRAWHAIREDEDVARAMGINLRNYKLLAFAIGASFGGVAG 264

Query: 253 AMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQ 312
           A+FGAFQGFVSPESF+L ES+ ++AMVVLGG+GHIPGVILGAVLL+ALPE+LR  A P+Q
Sbjct: 265 ALFGAFQGFVSPESFTLQESIAVLAMVVLGGMGHIPGVILGAVLLTALPELLRSQAAPVQ 324

Query: 313 AMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSPEHG 351
               G   +D  +LRQL   LA++++MLLRP+G+WP+   G
Sbjct: 325 QALFGEVLIDPEVLRQLFYGLALVLVMLLRPQGIWPARHQG 365


Lambda     K      H
   0.328    0.144    0.430 

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: 423
Number of extensions: 12
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 368
Length adjustment: 29
Effective length of query: 329
Effective length of database: 339
Effective search space:   111531
Effective search space used:   111531
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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