Align SSS sodium solute transporter (characterized, see rationale)
to candidate WP_057509052.1 ABB28_RS13160 sodium transporter
Query= uniprot:L0FZT5 (624 letters) >NCBI__GCF_001431535.1:WP_057509052.1 Length = 520 Score = 480 bits (1235), Expect = e-140 Identities = 250/507 (49%), Positives = 344/507 (67%), Gaps = 33/507 (6%) Query: 6 STLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAE 65 S LD I +VY + + WVSR K G K A++YFLA KSL WWAVGASL+AANISAE Sbjct: 4 SVLDTSIVLVYLAGVFVLAQWVSREKAGHAKDAKDYFLASKSLPWWAVGASLIAANISAE 63 Query: 66 HFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVST 125 IG SGSG+AIGL I++YEW+AA+ L+IV K+FLP+FL++G+YTMPQFL +R+ + T Sbjct: 64 QIIGMSGSGYAIGLAIASYEWMAALTLLIVGKWFLPVFLRNGIYTMPQFLEQRYGTRIRT 123 Query: 126 AFAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAWT 185 AVFWL +YVFVN+TS+ +LGA+A+ ++ G+ ++ + +F+ +Y +YGGL+AVA T Sbjct: 124 LMAVFWLGLYVFVNVTSILWLGAIAVSQVTGMDQMLAVVLIGVFALLYQLYGGLKAVALT 183 Query: 186 DVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDGLG 245 D+VQV +LV GGL+ T L L +G G GI AGM L+ HF MI+ + + Sbjct: 184 DIVQVSLLVLGGLLVTGLTLSQLGEGAGIVAGMQRLWEAHPGHFEMILSKDNLF------ 237 Query: 246 GSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKLLM 305 ++DLPG++V++GG+W+ NL YWGFNQYIIQ+ LAAK I EA+KG+LFA +LKLLM Sbjct: 238 -----YKDLPGISVLVGGLWIMNLSYWGFNQYIIQRALAAKDIGEAQKGVLFAAFLKLLM 292 Query: 306 PIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIRGLA 365 P+IVV+PGIAA + LA L+ P D+AYP ++R +P GI G+ Sbjct: 293 PLIVVVPGIAAVM---------LAPGLDAP----------DQAYPTMMR-LLPTGILGMV 332 Query: 366 FAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIAMIVA 425 FAAL AAIV+SLAS INS +TIFT+D Y P+ + LVR GRI A V + + ++ A Sbjct: 333 FAALVAAIVASLASKINSVATIFTLDFYAQRKGPH-DEATLVRVGRIAAAVTVVLGILAA 391 Query: 426 -PQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGIVFKIF 484 P L S DQ FQYIQEYTG+ PG+VV+F +GL W++A + AL A+ + +V K+ Sbjct: 392 KPLLGSFDQAFQYIQEYTGFFTPGIVVIFLLGLFWKRANEAGALAAAVGSFVLSVVLKLA 451 Query: 485 YPEMPFLLRMGYVFIILCFIASLISFA 511 +P +PF+ R+G VF++ +A +S A Sbjct: 452 WPSLPFIDRVGLVFLLALLLAVGVSLA 478 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: 1027 Number of extensions: 51 Number of successful extensions: 6 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: 624 Length of database: 520 Length adjustment: 36 Effective length of query: 588 Effective length of database: 484 Effective search space: 284592 Effective search space used: 284592 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 24 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