Align SSS sodium solute transporter (characterized, see rationale)
to candidate WP_057509052.1 ABB28_RS13160 sodium transporter
Query= uniprot:L0FZF3 (547 letters) >NCBI__GCF_001431535.1:WP_057509052.1 Length = 520 Score = 544 bits (1402), Expect = e-159 Identities = 282/549 (51%), Positives = 375/549 (68%), Gaps = 31/549 (5%) Query: 1 MTFNTLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNI 60 M + LD + + Y + + VSREK GH KD+KDYFLASK+LPWWAVGASLIA+NI Sbjct: 1 MQLSVLDTSIVLVYLAGVFVLAQWVSREKAGHAKDAKDYFLASKSLPWWAVGASLIAANI 60 Query: 61 SAEQFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGR 120 SAEQ IGMSGSG+A+GLAI++YEWMAA TLL+V +FLP++L+ GIYTMPQFL +RY R Sbjct: 61 SAEQIIGMSGSGYAIGLAIASYEWMAALTLLIVGKWFLPVFLRNGIYTMPQFLEQRYGTR 120 Query: 121 VRTVMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAV 180 +RT+MA+FWL +YVFVN+TS+L+LGA+++ + G+ ++ + +FA++Y +YGGLKAV Sbjct: 121 IRTLMAVFWLGLYVFVNVTSILWLGAIAVSQVTGMDQMLAVVLIGVFALLYQLYGGLKAV 180 Query: 181 AWTDVVQVVFLVAGGLATTYLALSLVGDG-DVWEGIGILRKAAPSHFSMIIEKGEMMIPD 239 A TD+VQV LV GGL T L LS +G+G + G+ L +A P HF MI+ K + Sbjct: 181 ALTDIVQVSLLVLGGLLVTGLTLSQLGEGAGIVAGMQRLWEAHPGHFEMILSKDNLF--- 237 Query: 240 GSGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLK 299 Y DLPG+SVL+GG+WI+NL+YWG NQYI QRALAAK +GEAQ G++FA FLK Sbjct: 238 --------YKDLPGISVLVGGLWIMNLSYWGFNQYIIQRALAAKDIGEAQKGVLFAAFLK 289 Query: 300 LLMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAF 359 LLMPLIVV+PGIAA ++ GL D+AYPT++ LLP G+ G+ F Sbjct: 290 LLMPLIVVVPGIAAVML----------------APGLDAPDQAYPTMMRLLPTGILGMVF 333 Query: 360 AALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVA- 418 AAL AAIV+SLAS NS +TIFT+D Y + + E V +GRI A V ++ + A Sbjct: 334 AALVAAIVASLASKINSVATIFTLDFYAQRKGPH-DEATLVRVGRIAAAVTVVLGILAAK 392 Query: 419 PQLRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVIT 478 P L DQAFQYIQEYTGF +PG+ IF+ G FWK+ AL AAV + LS K+ Sbjct: 393 PLLGSFDQAFQYIQEYTGFFTPGIVVIFLLGLFWKRANEAGALAAAVGSFVLSVVLKLAW 452 Query: 479 PNLPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKFKVGAVLICGI 538 P+LPFIDR+G+VFL+ +L + +SL +K + D +++T F VGA+ + I Sbjct: 453 PSLPFIDRVGLVFLLALLLAVGVSL-ATPAAPAKDVVRTDDVVYATRPSFNVGAIAVVAI 511 Query: 539 LVALYSVFW 547 L+ALY++FW Sbjct: 512 LIALYTLFW 520 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: 853 Number of extensions: 31 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: 520 Length adjustment: 35 Effective length of query: 512 Effective length of database: 485 Effective search space: 248320 Effective search space used: 248320 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 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