Align SSS sodium solute transporter (characterized, see rationale)
to candidate CA265_RS04220 CA265_RS04220 sodium:solute symporter
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__Pedo557:CA265_RS04220 Length = 550 Score = 268 bits (686), Expect = 3e-76 Identities = 175/564 (31%), Positives = 292/564 (51%), Gaps = 38/564 (6%) Query: 4 NTLDLVVFVAYCLLIITMGIVV-SREKKGHVKDSKDYFLASKALPWWAVGASLIASNISA 62 +T D+V+ +AY L I+T+G+ +R+KK S +YFLA K L W +G +L A+NIS Sbjct: 3 STTDIVITIAYILFIVTIGLWTGTRKKKNEETTSGEYFLAGKTLKWPMIGLALFATNISC 62 Query: 63 EQFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVR 122 + ++ SGF GL +EWMAA TL+++A+ F+P Y++ GI T+P FL RRY+ R Sbjct: 63 LHLVSLAQSGFDSGLLNGNFEWMAAFTLILLALLFIPFYIRSGISTLPDFLERRYNRACR 122 Query: 123 TVMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAW 182 +A +L + +++ G + LET+ G+ + I+ +AL +Y+I GGL+AV Sbjct: 123 DWLAFISILSAIIIHIAFSFLAGGIVLETLFGIDMYVSIVVIALLTGLYTIIGGLRAVVV 182 Query: 183 TDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKGEMMIPDGSG 242 T+ +Q + L+ G + TY A + VG D I + ++ A SMI I D SG Sbjct: 183 TETIQSLVLITGAIIITYFAWNKVGGWDHMTAI-LQKENAMDKLSMI-----RPIGDKSG 236 Query: 243 GSRDA-YLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLL 301 S A +L P L G+W YW +Q I QR L AK A+ G +F GF+K+L Sbjct: 237 MSWIAVFLGYPVL-----GIW-----YWCADQTIVQRVLGAKDENHARVGSLFCGFIKIL 286 Query: 302 MPLIVVIPGIAAYVIVQKGA-DASFIESMTDPVTGLAKSDRAYPTLL-HLLPPGLKGLAF 359 I V+PG+ AY++ + G D S ++++ + + Y ++ LLP GL G+ Sbjct: 287 PVFIFVLPGLFAYILYKSGTMDLSSLQTVGSNGETVLNTKGIYTLMITQLLPKGLVGILV 346 Query: 360 AALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAP 419 AAL + ++S +A NS +T+ + D+YK F S+ K V++GR +A +A ++ + P Sbjct: 347 AALLSGLMSQIAGALNSIATLSSYDLYKR-FKPETSDKKLVSVGRWSAGIALTVSIGLLP 405 Query: 420 QLRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAA---------LTAAVLTIPL 470 L + F I + ++P + +F+ G FWKK ++ A + A V + Sbjct: 406 LLNSYESLFNGINDVIAHIAPPITCVFLLGVFWKKASAKGAQYTLLLGSIIGAGVFVVNK 465 Query: 471 SAAFKVITPNLPFIDRMGVVFLVLSVLIIAIS-LYEGKGKDSKKAI-------EVDAELF 522 + I +PF+ +F + ++ + S +Y K + + + ++ + Sbjct: 466 VYGTETIIGQIPFMMMAFYLFCICVLIQVVFSHIYPVKHTAQSETLYWTSIWEPLKSKGW 525 Query: 523 STSTKFKVGAVLICGILVALYSVF 546 S +K +VL+ I+ LY F Sbjct: 526 SGIGNYKFLSVLLLAIMGVLYVYF 549 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: 691 Number of extensions: 36 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: 547 Length of database: 550 Length adjustment: 36 Effective length of query: 511 Effective length of database: 514 Effective search space: 262654 Effective search space used: 262654 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 Apr 09 2024. 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