Align SSS sodium solute transporter (characterized, see rationale)
to candidate Ga0059261_1623 Ga0059261_1623 transporter, SSS family
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__Korea:Ga0059261_1623 Length = 549 Score = 459 bits (1180), Expect = e-133 Identities = 252/580 (43%), Positives = 360/580 (62%), Gaps = 66/580 (11%) Query: 6 STLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAE 65 S +D ++ IVYA+ I ++ WVSR K G K +YFLA KSL WWA+GASL+AANISAE Sbjct: 5 SHIDLIVVIVYAIGIFALAQWVSREKAGHAKDTSDYFLASKSLPWWAIGASLIAANISAE 64 Query: 66 HFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVST 125 +G SGSG+AIGL I++YEW+AA+ L+IV K+FLPIFLK+ +YTMPQFL +RF + T Sbjct: 65 QIVGMSGSGYAIGLAIASYEWMAALTLLIVGKWFLPIFLKNEIYTMPQFLEQRFGPTIRT 124 Query: 126 AFAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAWT 185 AVFWL +Y+FVNLTS+ +LG++A+ ++ G+ + GL F+ +Y + GGL+AVA T Sbjct: 125 VMAVFWLALYIFVNLTSILWLGSIAVTQVAGVDQDIALFGLGAFALVYQLRGGLKAVALT 184 Query: 186 DVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDGLG 245 D+VQV +LV GGL+ ++L L +G G+ G + L + F MI+ PD Sbjct: 185 DIVQVTLLVLGGLVISYLTLSKIGGDAGVMGGFTRLTTELPGKFDMIL------APDN-- 236 Query: 246 GSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKLLM 305 ++DLPGL+V++GGMW+ NL YWGFNQYIIQ+ LAAKS+ EA+KG++FA +LKLLM Sbjct: 237 ---PFYKDLPGLSVLIGGMWIANLSYWGFNQYIIQRALAAKSLSEAQKGVVFAAFLKLLM 293 Query: 306 PIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIRGLA 365 P+I+V+PGIAA +L D + K D+AYP ++R +P G+ GL Sbjct: 294 PVIIVLPGIAAVILAPD-------------------LAKPDQAYPTMMR-LLPVGLLGLV 333 Query: 366 FAALAAAIVSSLASMINSTSTIFTMDIYK----VYFKPN---------------ANNHQL 406 FAAL AAI++S AS INS +TIFT+D+Y V + A+ QL Sbjct: 334 FAALVAAIIASTASKINSIATIFTLDLYAKAKGVQSRAQDAATASASGDSGLTAAHEKQL 393 Query: 407 VRTGRIVAVVALAIAMIVA-PQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATAS 465 VR GR AVVA +A+ A P L SLDQ FQYIQE++G++ PG+ V+F +GL W +AT + Sbjct: 394 VRVGRTTAVVATLLAIFTARPLLGSLDQAFQYIQEFSGFVTPGITVIFLLGLFWPRATEA 453 Query: 466 AALWTAIATIPAGIVFKIFYP----------EMPFLLRMGYVFIILCFIASLISFAEKKK 515 AL A+A++ +F ++P +PF+ RM VF + +A ++S Sbjct: 454 GALTGAVASVLLSFLF--WFPADWGGIATLNAVPFMNRMMIVFFVSLALAVVVSLVRP-- 509 Query: 516 FANPDYKTNKQAAKTVASSYFFIILGIICAVLGFALFNSY 555 A D + ++ F + G+I ++ AL+ ++ Sbjct: 510 -APADSNRITMQGVSFGTTTSFNVAGVIIIMILIALYATW 548 Score = 32.7 bits (73), Expect = 4e-05 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 3/76 (3%) Query: 548 GFALFNSYEHVGIESIFMIAALFLMLGTILYTNVKMETADPKSFNTDPVLFNTTSSFNLG 607 G A N+ + I +L L ++ + V+ AD V F TT+SFN+ Sbjct: 477 GIATLNAVPFMNRMMIVFFVSLAL---AVVVSLVRPAPADSNRITMQGVSFGTTTSFNVA 533 Query: 608 AAGIILIVGLLYYFFW 623 II+I+ LY +W Sbjct: 534 GVIIIMILIALYATWW 549 Lambda K H 0.327 0.142 0.427 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: 1004 Number of extensions: 46 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 624 Length of database: 549 Length adjustment: 37 Effective length of query: 587 Effective length of database: 512 Effective search space: 300544 Effective search space used: 300544 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 (21.7 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