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.
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:
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