GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00890 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS07275 BWI76_RS07275 ABC
           transporter
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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