Align SSS sodium solute transporter (characterized, see rationale)
to candidate Echvi_3497 Echvi_3497 transporter, SSS family
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__Cola:Echvi_3497 Length = 527 Score = 255 bits (652), Expect = 3e-72 Identities = 169/554 (30%), Positives = 293/554 (52%), Gaps = 51/554 (9%) Query: 6 LDLVVFVAYCLLIITMGIVVSREKKGHVKDSKD-YFLASKALPWWAVGASLIASNISAEQ 64 + ++ F+A+ LL+ + +R++ DS+D YFL ++L + S+I +NIS E Sbjct: 3 ITILTFIAFTLLVAVYAWLKTRKEN---LDSEDGYFLGGRSLTGVVIAGSMIMTNISTEH 59 Query: 65 FIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRTV 124 +GM+GS + G I +E +A L+V A++F+P YLK G+ T+PQ+L R+D R++ Sbjct: 60 LVGMNGSSYKNGFVIVAWEVTSALALIVAAVYFVPRYLKMGLTTVPQYLENRFDAGTRSL 119 Query: 125 MAIFWLLIYVFVNLTSVLYLGALSLETIMGVP----------LTYGIIGLALFAMVYSIY 174 +A F L+ + L VLY GA++LE++ + L Y ++ + +Y+I+ Sbjct: 120 VAFFLLISFAVTLLPIVLYTGAINLESLFNISDTLNISQEQGLWYTVLAVGGIGSIYAIF 179 Query: 175 GGLKAVAWTDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKGE 234 GGLKAVA +D + L+ GL +AL ++GD + G+ + + +P F+++ Sbjct: 180 GGLKAVAVSDTINGYGLLLAGLMVPVIALFMIGDNNPLLGLERVFENSPEKFNVV----- 234 Query: 235 MMIPDGSGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVF 294 G +D+ L S L G+ I L +W NQ I QRAL AK+L EAQ G+++ Sbjct: 235 --------GGKDSVLP---FSTLFTGLIINQLYFWCMNQTIIQRALGAKNLKEAQKGLLY 283 Query: 295 AGFLKLLMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLL-HLLPPG 353 G LKLL+P I+V+PG+ + F + + + D YP L+ +LP G Sbjct: 284 TGALKLLVPFIIVLPGVIGFYF--------FGDRLYE------NQDMVYPELVKKVLPVG 329 Query: 354 LKGLAFAALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFII 413 L G+ A + A++S+ S+ NS STIF+IDIYK S G+ V G+++A + I Sbjct: 330 LTGVFAAVIMGAVLSTFNSVLNSASTIFSIDIYKRLIRPGASAGQLVKAGKLSATILAIT 389 Query: 414 AAIVAPQLRQLDQA-FQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAV--LTIPL 470 + + AP + + FQ +Q+ G + +I + GFF K + AA A V LT + Sbjct: 390 SMVAAPMVANAPEGLFQLLQQLNGIFFIPIASIMLAGFFTKWVSPLAAKVALVTGLTFYV 449 Query: 471 SAAFKVITPNLPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKF-K 529 F V + F+ G+ F++ +++ +S+ K ++K + + A++ + K+ Sbjct: 450 LTTF-VFDIGIHFVHIWGIEFVLNVLIMYVVSVAWPMAKPTEKTL-ISAKINTDKWKYAS 507 Query: 530 VGAVLICGILVALY 543 + ++++ I V +Y Sbjct: 508 LVSIILVIITVVIY 521 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: 659 Number of extensions: 27 Number of successful extensions: 4 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: 527 Length adjustment: 35 Effective length of query: 512 Effective length of database: 492 Effective search space: 251904 Effective search space used: 251904 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 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