Align SSS sodium solute transporter (characterized, see rationale)
to candidate Ga0059261_1623 Ga0059261_1623 transporter, SSS family
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__Korea:Ga0059261_1623 Length = 549 Score = 519 bits (1336), Expect = e-151 Identities = 289/571 (50%), Positives = 368/571 (64%), Gaps = 57/571 (9%) Query: 6 LDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQF 65 +DL+V + Y + I + VSREK GH KD+ DYFLASK+LPWWA+GASLIA+NISAEQ Sbjct: 7 IDLIVVIVYAIGIFALAQWVSREKAGHAKDTSDYFLASKSLPWWAIGASLIAANISAEQI 66 Query: 66 IGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRTVM 125 +GMSGSG+A+GLAI++YEWMAA TLL+V +FLPI+LK IYTMPQFL +R+ +RTVM Sbjct: 67 VGMSGSGYAIGLAIASYEWMAALTLLIVGKWFLPIFLKNEIYTMPQFLEQRFGPTIRTVM 126 Query: 126 AIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAWTDV 185 A+FWL +Y+FVNLTS+L+LG++++ + GV + GL FA+VY + GGLKAVA TD+ Sbjct: 127 AVFWLALYIFVNLTSILWLGSIAVTQVAGVDQDIALFGLGAFALVYQLRGGLKAVALTDI 186 Query: 186 VQVVFLVAGGLATTYLALSLV-GDGDVWEGIGILRKAAPSHFSMIIEKGEMMIPDGSGGS 244 VQV LV GGL +YL LS + GD V G L P F MI + PD Sbjct: 187 VQVTLLVLGGLVISYLTLSKIGGDAGVMGGFTRLTTELPGKFDMI------LAPD----- 235 Query: 245 RDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLLMPL 304 Y DLPGLSVLIGGMWI NL+YWG NQYI QRALAAKSL EAQ G+VFA FLKLLMP+ Sbjct: 236 NPFYKDLPGLSVLIGGMWIANLSYWGFNQYIIQRALAAKSLSEAQKGVVFAAFLKLLMPV 295 Query: 305 IVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAFAALTA 364 I+V+PGIAA ++ LAK D+AYPT++ LLP GL GL FAAL A Sbjct: 296 IIVLPGIAAVIL----------------APDLAKPDQAYPTMMRLLPVGLLGLVFAALVA 339 Query: 365 AIVSSLASMANSTSTIFTIDIYKEFFNKN-------------------VSEGKQVTIGRI 405 AI++S AS NS +TIFT+D+Y + E + V +GR Sbjct: 340 AIIASTASKINSIATIFTLDLYAKAKGVQSRAQDAATASASGDSGLTAAHEKQLVRVGRT 399 Query: 406 TAVVAFIIAAIVA-PQLRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAA 464 TAVVA ++A A P L LDQAFQYIQE++GFV+PG+ IF+ G FW + T ALT A Sbjct: 400 TAVVATLLAIFTARPLLGSLDQAFQYIQEFSGFVTPGITVIFLLGLFWPRATEAGALTGA 459 Query: 465 VLTIPLSAAF-------KVITPN-LPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIE 516 V ++ LS F + T N +PF++RM +VF V L + +SL DS + I Sbjct: 460 VASVLLSFLFWFPADWGGIATLNAVPFMNRMMIVFFVSLALAVVVSLVRPAPADSNR-IT 518 Query: 517 VDAELFSTSTKFKVGAVLICGILVALYSVFW 547 + F T+T F V V+I IL+ALY+ +W Sbjct: 519 MQGVSFGTTTSFNVAGVIIIMILIALYATWW 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: 810 Number of extensions: 33 Number of successful extensions: 7 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: 549 Length adjustment: 36 Effective length of query: 511 Effective length of database: 513 Effective search space: 262143 Effective search space used: 262143 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