Align KguT (characterized, see rationale)
to candidate BWI76_RS26955 BWI76_RS26955 MFS transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__Koxy:BWI76_RS26955 Length = 426 Score = 612 bits (1579), Expect = e-180 Identities = 293/412 (71%), Positives = 342/412 (83%), Gaps = 1/412 (0%) Query: 7 APRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQ 66 A +RWWYIMPIVFITYSLAYLDRAN+ FA+A+G+ +DL IT +SSLLGALFFLGYFFFQ Sbjct: 7 ATKRWWYIMPIVFITYSLAYLDRANFSFASAAGITEDLGITKGISSLLGALFFLGYFFFQ 66 Query: 67 VPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIY 126 +PGAIYAE+RSV+KLIF+ LILWG A+LTGMV ++ L AIRF+LGVVEAAVMPAMLIY Sbjct: 67 IPGAIYAERRSVRKLIFICLILWGACASLTGMVHNIPALAAIRFILGVVEAAVMPAMLIY 126 Query: 127 LCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFIWW 186 + +WFT++ERSRANTFLILGNPVT+LWMSVVSGYL++ F WR MFIIEG+PAV+WAF WW Sbjct: 127 ISNWFTKSERSRANTFLILGNPVTVLWMSVVSGYLIQAFGWREMFIIEGVPAVIWAFCWW 186 Query: 187 RLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWSIG 246 LV D+P Q +WL EK AL+E L EQQGIKPV+NY EAFRS V++L +QYF WSIG Sbjct: 187 VLVKDKPSQVNWLAESEKAALQEQLEREQQGIKPVRNYGEAFRSRNVVLLCMQYFAWSIG 246 Query: 247 VYGFVLWLPSILKQAAA-LDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPL 305 VYGFVLWLPSI++ + +V GWLS+VPYL A +AM+ VSWASD+MQ RK FVWP L Sbjct: 247 VYGFVLWLPSIIRSGGENMGMVEVGWLSSVPYLAATIAMIVVSWASDKMQNRKLFVWPLL 306 Query: 306 LIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALIN 365 LIAA AF GS+ +G HFW SYTLLVIAGA MYAPYGPFFAI+PE+LP NVAGGAMALIN Sbjct: 307 LIAAFAFIGSWAVGANHFWVSYTLLVIAGAAMYAPYGPFFAIIPEMLPRNVAGGAMALIN 366 Query: 366 SMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQAR 417 SMGALGSF GSW VGYLNG TG P ASY+FM AL V+V LT ++ P+ + Sbjct: 367 SMGALGSFFGSWFVGYLNGTTGSPSASYIFMGVALFVSVWLTLIVKPANNQK 418 Lambda K H 0.328 0.140 0.457 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: 828 Number of extensions: 39 Number of successful extensions: 3 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: 425 Length of database: 426 Length adjustment: 32 Effective length of query: 393 Effective length of database: 394 Effective search space: 154842 Effective search space used: 154842 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 (21.8 bits) S2: 51 (24.3 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