GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacH in Halococcus hamelinensis 100A6

Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate WP_007695788.1 C447_RS16060 sugar ABC transporter permease

Query= uniprot:D4GP36
         (317 letters)



>NCBI__GCF_000336675.1:WP_007695788.1
          Length = 324

 Score =  412 bits (1058), Expect = e-120
 Identities = 197/296 (66%), Positives = 238/296 (80%)

Query: 22  SKLRYFLNSDFVRSAPYWGIPFVLMSIAVYGGTGYNFAISFTDYEGLGTPDYSTLDLEMY 81
           S+LR    SDFVRS PYW +PFV+M   VYGG G+N  +S TDY G G+ DY  LD EMY
Sbjct: 29  SRLRSISESDFVRSMPYWFVPFVIMGFFVYGGIGWNLLVSLTDYTGFGSADYGDLDFEMY 88

Query: 82  AQALSSDAFIAAAQNNLVLLVGFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSF 141
            QALSS   IAA++N  VLLV FT +CLVLGL LAI+LD  IRF E+ QT+YLLPM+LSF
Sbjct: 89  VQALSSPDVIAASRNTFVLLVVFTAVCLVLGLALAIVLDRQIRFKEQIQTIYLLPMALSF 148

Query: 142 VVTAQLWLWMFNVESGILNLVVTTLGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYL 201
           VVTAQ WLWM+N  SG++N+++  +G   + ++G+P   LGAVI ALIWQFSGYTM+VYL
Sbjct: 149 VVTAQFWLWMYNYNSGVINIILDAVGIGRIQFIGDPRFVLGAVIFALIWQFSGYTMIVYL 208

Query: 202 AGLQSIPDDQFEAARVDGASITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVG 261
           +GLQSIP DQFEAA  DGAS  + Y R+I+PQLK ASVSAAVVLM+FALKAFTFLY++ G
Sbjct: 209 SGLQSIPQDQFEAAATDGASTVKIYWRVIIPQLKSASVSAAVVLMIFALKAFTFLYSMFG 268

Query: 262 RYRPPNGTDILATLMVRRAFKFGEWAYSAAIATMLLIMALGVIGPYLYYQYKQGGL 317
            YRPPNG+DILATLMVR+AFKF EW+Y+AA+AT+LL+MAL VIGPYLYYQY++G L
Sbjct: 269 TYRPPNGSDILATLMVRQAFKFQEWSYAAAVATLLLLMALVVIGPYLYYQYQRGSL 324


Lambda     K      H
   0.326    0.140    0.424 

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: 374
Number of extensions: 11
Number of successful extensions: 1
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: 317
Length of database: 324
Length adjustment: 28
Effective length of query: 289
Effective length of database: 296
Effective search space:    85544
Effective search space used:    85544
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 (21.6 bits)
S2: 48 (23.1 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