Align SSS sodium solute transporter (characterized, see rationale)
to candidate CA265_RS06755 CA265_RS06755 sodium transporter
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__Pedo557:CA265_RS06755 Length = 542 Score = 489 bits (1260), Expect = e-142 Identities = 266/555 (47%), Positives = 364/555 (65%), Gaps = 38/555 (6%) Query: 6 STLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAE 65 S DY +F++Y + + + G WV R+KK ++YFLA+ SLTWWA+GAS++A+NISAE Sbjct: 5 SAFDYAVFLMYFVIVSAYGYWVYRSKKKKRTDTKDYFLAEGSLTWWAIGASIIASNISAE 64 Query: 66 HFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVST 125 HFIG SGSGFA+GL I++YEW+AA LIIVA +FLPI++K+ +YTMPQFLS R+N VST Sbjct: 65 HFIGMSGSGFAMGLAIASYEWMAAATLIIVAIFFLPIYIKNKIYTMPQFLSNRYNNTVST 124 Query: 126 AFAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAWT 185 AVFWLLVYVFVNLTS+ +LGA+A++ I G+P II L IFS I ++ GG++ + +T Sbjct: 125 LMAVFWLLVYVFVNLTSIFFLGAIAIETITGVPFNICIIFLAIFSAIITL-GGMKVIGYT 183 Query: 186 DVVQVIILVAGGLITTFLALDAVGM---GDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPD 242 DV+QV +LVAGGLIT ++AL V + A + L ++A DHF MI +G Sbjct: 184 DVIQVFVLVAGGLITCYMALKLVSEKLDAPSVLASLPLLRSEASDHFHMIFSKGDKF--- 240 Query: 243 GLGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLK 302 + +LPG+AV++GG+W+ NL YWG NQYI+Q+ L A ++ + GL+FA +LK Sbjct: 241 --------YNELPGIAVLVGGLWINNLNYWGCNQYIVQRALGA-DLKTGRNGLIFAAFLK 291 Query: 303 LLMPIIVVIPGIAAYVLIND--YSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNG 360 LL+P+IVVIPGIAAYVL + E L A + K D AYP +L N +P G Sbjct: 292 LLIPVIVVIPGIAAYVLYQRGYFHSEMLDA---------AGVVKPDHAYP-VLMNLLPAG 341 Query: 361 IRGLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAI 420 I+GLAFAAL AAIV+SLA NS +TIFT+DIYK + KP A+ +LV GR V+A I Sbjct: 342 IKGLAFAALTAAIVASLAGKCNSIATIFTLDIYKKFIKPEASETRLVSVGRWSVVIASLI 401 Query: 421 AMIVAPQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGIV 480 A+I+AP L S DQV+Q+IQEY G+I PGV +F +G W++ T+ AAL A+ TIP + Sbjct: 402 AIIIAPALRSFDQVYQFIQEYVGFISPGVFAIFLLGFFWKKTTSRAALTAALLTIPLSTL 461 Query: 481 FKIFYP--------EMPFLLRMGYVFIILCFIASLISFAEKKKFANPDYKTNKQAAKTVA 532 FK F P +PFL RM +VF+I+ + +++ + K NP + V Sbjct: 462 FK-FLPAVTNGAIAPIPFLNRMSWVFMIIIGLMIVVTLTDPKSKDNPQGLEIDSSMFKVT 520 Query: 533 SSYFFIILGIICAVL 547 + F I +IC +L Sbjct: 521 PA-FTIASVMICGIL 534 Lambda K H 0.327 0.142 0.427 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: 1081 Number of extensions: 46 Number of successful extensions: 6 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: 624 Length of database: 542 Length adjustment: 36 Effective length of query: 588 Effective length of database: 506 Effective search space: 297528 Effective search space used: 297528 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 (21.7 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