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

GapMind for catabolism of small carbon sources

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

Align SSS sodium solute transporter (characterized, see rationale)
to candidate Echvi_1880 Echvi_1880 transporter, SSS family

Query= uniprot:L0FZF3
         (547 letters)



>lcl|FitnessBrowser__Cola:Echvi_1880 Echvi_1880 transporter, SSS
           family
          Length = 624

 Score =  609 bits (1570), Expect = e-178
 Identities = 313/548 (57%), Positives = 403/548 (73%), Gaps = 16/548 (2%)

Query: 3   FNTLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISA 62
           F+TLD V+F+ Y L I+++G+ VSR KKG  K +++YFLA K+L WWAVGASL+A+NISA
Sbjct: 5   FSTLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISA 64

Query: 63  EQFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVR 122
           E FIG SGSGFA+GL IS YEW+AA  L++VA +FLPI+LK G+YTMPQFL+ R++  V 
Sbjct: 65  EHFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVS 124

Query: 123 TVMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAW 182
           T  A+FWLL+YVFVNLTSV YLGAL+L+ IMG+PL YGIIGL +F+ +YSIYGGL+AVAW
Sbjct: 125 TAFAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAW 184

Query: 183 TDVVQVVFLVAGGLATTYLALSLVGDGD-VWEGIGILRKAAPSHFSMIIEKGEMMIPDGS 241
           TDVVQV+ LVAGGL TT+LAL  VG GD ++ G+  L   A  HF MI+ +G +M+PDG 
Sbjct: 185 TDVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDGL 244

Query: 242 GGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLL 301
           GGSRDA+ DLPGL+V++GGMW+ NL YWG NQYI Q+ LAAKS+ EA+ G++FAG+LKLL
Sbjct: 245 GGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKLL 304

Query: 302 MPLIVVIPGIAAYVIVQKGAD---ASFIESMTDPVTGLAKSDRAYPTLL-HLLPPGLKGL 357
           MP+IVVIPGIAAYV++   +    A+ +    + +  + KSD AYP LL + +P G++GL
Sbjct: 305 MPIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIRGL 364

Query: 358 AFAALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIV 417
           AFAAL AAIVSSLASM NSTSTIFT+DIYK +F  N +  + V  GRI AVVA  IA IV
Sbjct: 365 AFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIAMIV 424

Query: 418 APQLRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVI 477
           APQL  LDQ FQYIQEYTG++ PGV  +F  G  W++ T++AAL  A+ TIP    FK+ 
Sbjct: 425 APQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGIVFKIF 484

Query: 478 TPNLPFIDRMGVVFLVLSVLIIAISLYEGKG------KDSKKAIEVDAELFSTSTKFKVG 531
            P +PF+ RMG VF++L  +   IS  E K       K +K+A +  A     S+ F + 
Sbjct: 485 YPEMPFLLRMGYVFIILCFIASLISFAEKKKFANPDYKTNKQAAKTVA-----SSYFFII 539

Query: 532 AVLICGIL 539
             +IC +L
Sbjct: 540 LGIICAVL 547



 Score = 30.0 bits (66), Expect = 3e-04
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 3/61 (4%)

Query: 490 VFLVLSV-LIIAISLYEGKGKDSK--KAIEVDAELFSTSTKFKVGAVLICGILVALYSVF 546
           +F++ ++ L++   LY     ++   K+   D  LF+T++ F +GA  I  I+  LY  F
Sbjct: 563 IFMIAALFLMLGTILYTNVKMETADPKSFNTDPVLFNTTSSFNLGAAGIILIVGLLYYFF 622

Query: 547 W 547
           W
Sbjct: 623 W 623


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: 1003
Number of extensions: 43
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 547
Length of database: 624
Length adjustment: 36
Effective length of query: 511
Effective length of database: 588
Effective search space:   300468
Effective search space used:   300468
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources