GapMind for catabolism of small carbon sources

 

Alignments for a candidate for exuT in Amantichitinum ursilacus IGB-41

Align Hexuronate transporter (characterized)
to candidate WP_053935923.1 WG78_RS01030 MFS transporter

Query= SwissProt::P0AA78
         (432 letters)



>NCBI__GCF_001294205.1:WP_053935923.1
          Length = 432

 Score =  517 bits (1331), Expect = e-151
 Identities = 239/428 (55%), Positives = 325/428 (75%), Gaps = 6/428 (1%)

Query: 1   MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTV 60
           M K+KG+RW+M+ +VT G ++ YL RNT++ AAPT+M +L+++T++YSY++ A+ A Y +
Sbjct: 1   MGKVKGMRWWMVGMVTAGLIVNYLARNTLSVAAPTMMHDLHMTTKEYSYVVVAWQACYAL 60

Query: 61  MQPVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGL 120
           MQPVAGY+LD +GTKIG+A+FA  W+V C A A AG+W GLAV RG +G  EAA IPAG+
Sbjct: 61  MQPVAGYILDAIGTKIGFAIFACAWSVACAAAAFAGNWQGLAVFRGMLGLTEAAGIPAGV 120

Query: 121 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMA 180
           KA++EWFPA+ERS+A+G+FN+GSSIGA++APPLVVWAI+  SW+ AF+I G L  IW   
Sbjct: 121 KATTEWFPARERSVAIGWFNIGSSIGALLAPPLVVWAIMAGSWEWAFVIVGVLGGIWTAL 180

Query: 181 WLIFYKHPRDQKHLTDEERDYIINGQEAQHQ---VSTAKKMSVGQILRNRQFWGIALPRF 237
           W++FYKHP++QK L+D ERDYI+ GQEAQ++    + A +     I+++R F  IA+PRF
Sbjct: 181 WMLFYKHPKNQKALSDAERDYILAGQEAQYREEGAAVAPRARWTAIVKSRNFRAIAIPRF 240

Query: 238 LAEPAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVN 297
           L+EPAW TFNAWIPL+M      NLKEIAMFAW+P L AD+GC+LGGYL P F ++  V 
Sbjct: 241 LSEPAWQTFNAWIPLYMATERHMNLKEIAMFAWLPFLAADMGCVLGGYLSPFFHKYCNVG 300

Query: 298 LIVSRKMVVTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRN 357
           L  SRK+V+  GAV MIGP  IGL ++PY AI LLC+GGFAHQ LSGAL  ++SD+FG+N
Sbjct: 301 LFQSRKLVMITGAVCMIGPACIGLVSSPYTAIALLCVGGFAHQTLSGALYAITSDMFGKN 360

Query: 358 EVATANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTVLQNK-- 415
           EVATA GL GM  +L +TLF L  G L   +G+SPLF +LA+FD++ A+ +  + + +  
Sbjct: 361 EVATATGLGGMCGYLGATLFTLFFGVLVTQVGYSPLFVMLAIFDVIAAITLCLLARERTT 420

Query: 416 -PAIEVAQ 422
            PA+ +A+
Sbjct: 421 PPALPLAE 428


Lambda     K      H
   0.326    0.138    0.437 

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: 682
Number of extensions: 29
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: 432
Length of database: 432
Length adjustment: 32
Effective length of query: 400
Effective length of database: 400
Effective search space:   160000
Effective search space used:   160000
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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