Align SSS sodium solute transporter (characterized, see rationale)
to candidate 5209833 Shew_2286 SSS family solute/sodium (Na+) symporter (RefSeq)
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__PV4:5209833 Length = 519 Score = 535 bits (1377), Expect = e-156 Identities = 275/545 (50%), Positives = 377/545 (69%), Gaps = 31/545 (5%) Query: 5 TLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQ 64 TLD+ + + Y L ++ + + +SR+ K H +D+KDYFLA KALPWWA+GASLIASNISAEQ Sbjct: 4 TLDIGILLVYALGLLGLALWISRQDKRHERDTKDYFLAGKALPWWAIGASLIASNISAEQ 63 Query: 65 FIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRTV 124 IGMSGSG+A+GLAI++YEWMAA TL++V + LPI++K IYTMPQ+L +R+D RV+T Sbjct: 64 IIGMSGSGYAIGLAIASYEWMAAITLILVGKYMLPIFIKNEIYTMPQYLEQRFDKRVKTT 123 Query: 125 MAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAWTD 184 +A+FWL +Y+ VNLT+VL+LG L++ET+ G+ YG++ LALF++ YS+YGGLKAVA+TD Sbjct: 124 LALFWLSVYILVNLTAVLWLGGLAIETVAGIDWLYGMVFLALFSLAYSLYGGLKAVAYTD 183 Query: 185 VVQVVFLVAGGLATTYLALSLVGDGD-VWEGIGILRKAAPSHFSMIIEKGEMMIPDGSGG 243 ++QVV L+ GGL +YLAL V DG V G L A P HF MI+ + Sbjct: 184 IIQVVLLIFGGLLLSYLALDRVADGQGVLAGFDRLSSALPEHFEMILSQ----------- 232 Query: 244 SRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLLMP 303 S Y+ LPG+SVL+GG+WI+N++YWG NQYI QRALAAKS+ EAQ G+ FA +LKLLMP Sbjct: 233 SNPHYMSLPGISVLVGGLWIMNISYWGFNQYIIQRALAAKSVAEAQKGIAFAAYLKLLMP 292 Query: 304 LIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAFAALT 363 LIVV+PGIAA ++ GL D+AYP+++ L+P G+KGL FAAL Sbjct: 293 LIVVLPGIAAVLL----------------YPGLESPDQAYPSMMALMPAGVKGLVFAALV 336 Query: 364 AAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVA-PQLR 422 AAIVSSLASM NS STIFT+DIY SEG V +GR++++++ +IA ++A P L Sbjct: 337 AAIVSSLASMTNSISTIFTMDIY-AMLRPAKSEGHYVLVGRLSSLISLLIALVMAQPLLG 395 Query: 423 QLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITPNLP 482 + +QAFQYIQE+TG +PG+ IF+ G FW++ TS AL AA+ + S + P LP Sbjct: 396 EFEQAFQYIQEFTGVFTPGIVVIFLTGMFWRRATSQGALAAALGSAIFSFGLRFYWPELP 455 Query: 483 FIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKFKVGAVLICGILVAL 542 F+DR+G+VFL+ L + +SL G+ + ++ + F T F V A+ + IL L Sbjct: 456 FMDRIGLVFLLCLALSVLVSLM-GRSLEEGASVALGGVSFKTGRAFNVSALGVVVILNFL 514 Query: 543 YSVFW 547 Y +W Sbjct: 515 YVTWW 519 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: 866 Number of extensions: 42 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: 519 Length adjustment: 35 Effective length of query: 512 Effective length of database: 484 Effective search space: 247808 Effective search space used: 247808 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: 52 (24.6 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