GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cola:Echvi_1880
          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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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