Align SSS sodium solute transporter (characterized, see rationale)
to candidate CA265_RS19720 CA265_RS19720 sodium transporter
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__Pedo557:CA265_RS19720 Length = 558 Score = 578 bits (1489), Expect = e-169 Identities = 307/571 (53%), Positives = 402/571 (70%), Gaps = 46/571 (8%) Query: 4 NTLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAE 63 +T D +VF Y +++ G+ + +KK SKDYFLA +L WWA+GASLIASNISAE Sbjct: 7 DTKDYIVFAIYFVIVAAYGLYIYNKKKSASTGSKDYFLAEGSLTWWAIGASLIASNISAE 66 Query: 64 QFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRT 123 QFIGMSGSGF +GLAI+TYEWMAA TL++VA+FF+P+YLK I TMPQFL++RY+G V Sbjct: 67 QFIGMSGSGFKMGLAIATYEWMAALTLVIVAVFFIPVYLKNKIATMPQFLHQRYNGTVAM 126 Query: 124 VMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAWT 183 +MA+FWLL+YV VNLTS+LYLGAL++ +I G LT+ + +A FA+V ++ GG+K + +T Sbjct: 127 IMAVFWLLLYVVVNLTSILYLGALAVSSISGFDLTFCMYAIAAFAIVITL-GGMKVIGYT 185 Query: 184 DVVQVVFLVAGGLATTYLALSLV----GDGDVWEGIGILRKAAPSHFSMIIEKGEMMIPD 239 DV+QV FL+ GGLATTYLAL+LV G ++EG ++ A HF MI++ PD Sbjct: 186 DVIQVFFLILGGLATTYLALNLVSTHYGTSGIFEGYSLMTSKASEHFHMILK------PD 239 Query: 240 GSGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLK 299 + Y+DLPGLSVL+GGMWIVNLNYWGCNQYITQRAL A L A+ G++FA FLK Sbjct: 240 -----NENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGA-DLKTARGGILFAAFLK 293 Query: 300 LLMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAF 359 LLMP+IVV+PGIAAYV+ + GA S E + D G DRAYP LL+LLP GLKGL+F Sbjct: 294 LLMPIIVVLPGIAAYVLYKDGAFQS--EMLQD---GSVNPDRAYPVLLNLLPAGLKGLSF 348 Query: 360 AALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAP 419 AALTAA+V+SLA ANS +TIFT+DIYK+ + SE V G+I VVA ++ ++AP Sbjct: 349 AALTAAVVASLAGKANSIATIFTLDIYKKVLKTDASEKNLVFTGKIAVVVAMVLGVVIAP 408 Query: 420 QLRQLDQ--AFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVI 477 L +D+ FQYIQEYTGFVSPG+FA+FI GFFWK+ TSNAAL A V LS KV+ Sbjct: 409 YL-GIDKKGGFQYIQEYTGFVSPGIFAMFILGFFWKRATSNAALFATVGGFGLSLLLKVL 467 Query: 478 TP---------------------NLPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIE 516 +PF+DRMG VF+ + ++ ISL+E + + K +E Sbjct: 468 PTWTDLSWLSGMGFSVKNGVGVYEIPFLDRMGFVFVFCVIGMVIISLFENRNGVNPKGLE 527 Query: 517 VDAELFSTSTKFKVGAVLICGILVALYSVFW 547 +D+++F T+T F VG+++I G+LVALYSV+W Sbjct: 528 IDSKMFKTTTGFAVGSLIIIGLLVALYSVYW 558 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: 948 Number of extensions: 48 Number of successful extensions: 8 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: 547 Length of database: 558 Length adjustment: 36 Effective length of query: 511 Effective length of database: 522 Effective search space: 266742 Effective search space used: 266742 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