GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Echvi_1871 in Echinicola vietnamensis KMM 6221, DSM 17526

Align SSS sodium solute transporter (characterized, see rationale)
to candidate Echvi_1871 Echvi_1871 transporter, SSS family

Query= uniprot:L0FZF3
         (547 letters)



>lcl|FitnessBrowser__Cola:Echvi_1871 Echvi_1871 transporter, SSS
           family
          Length = 547

 Score = 1061 bits (2743), Expect = 0.0
 Identities = 547/547 (100%), Positives = 547/547 (100%)

Query: 1   MTFNTLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNI 60
           MTFNTLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNI
Sbjct: 1   MTFNTLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNI 60

Query: 61  SAEQFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGR 120
           SAEQFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGR
Sbjct: 61  SAEQFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGR 120

Query: 121 VRTVMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAV 180
           VRTVMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAV
Sbjct: 121 VRTVMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAV 180

Query: 181 AWTDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKGEMMIPDG 240
           AWTDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKGEMMIPDG
Sbjct: 181 AWTDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKGEMMIPDG 240

Query: 241 SGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKL 300
           SGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKL
Sbjct: 241 SGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKL 300

Query: 301 LMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAFA 360
           LMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAFA
Sbjct: 301 LMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAFA 360

Query: 361 ALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAPQ 420
           ALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAPQ
Sbjct: 361 ALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAPQ 420

Query: 421 LRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITPN 480
           LRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITPN
Sbjct: 421 LRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITPN 480

Query: 481 LPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKFKVGAVLICGILV 540
           LPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKFKVGAVLICGILV
Sbjct: 481 LPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKFKVGAVLICGILV 540

Query: 541 ALYSVFW 547
           ALYSVFW
Sbjct: 541 ALYSVFW 547


Lambda     K      H
   0.326    0.140    0.414 

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: 1098
Number of extensions: 32
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: 547
Length of database: 547
Length adjustment: 36
Effective length of query: 511
Effective length of database: 511
Effective search space:   261121
Effective search space used:   261121
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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