Align KguT (characterized, see rationale)
to candidate PfGW456L13_2949 2-ketogluconate transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2949 Length = 430 Score = 702 bits (1813), Expect = 0.0 Identities = 339/419 (80%), Positives = 367/419 (87%) Query: 1 MQIDRLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFL 60 M+ LA RRWWYIMPIVFITYSLAYLDRANYGFAAASGMA DL ITP LSS+LGALFFL Sbjct: 1 MKTATLATRRWWYIMPIVFITYSLAYLDRANYGFAAASGMAADLMITPGLSSMLGALFFL 60 Query: 61 GYFFFQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVM 120 GYFFFQVPGAIYA+K SVKKLIFVSLILWG LATLTG+V + LI IRF+LGVVEAAVM Sbjct: 61 GYFFFQVPGAIYAQKHSVKKLIFVSLILWGSLATLTGIVSNAYWLIVIRFMLGVVEAAVM 120 Query: 121 PAMLIYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVL 180 PAMLIYLCHWFTRAERSRANTFLILGNPVT+LWMSVVSGYLV+H+ WRWMFI+EGLPAVL Sbjct: 121 PAMLIYLCHWFTRAERSRANTFLILGNPVTMLWMSVVSGYLVQHYSWRWMFIVEGLPAVL 180 Query: 181 WAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQY 240 WAFIWWRL DDRP QA WL QEK L ALAAEQ GIK VKNY EAFRSPKVIIL+LQ+ Sbjct: 181 WAFIWWRLADDRPSQAKWLNDQEKQDLESALAAEQVGIKAVKNYAEAFRSPKVIILALQF 240 Query: 241 FCWSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRF 300 FCWSIGVYGFVLWLPSILK A +D+V AGWLSA+PYL AV+ ML VSW SD++QKRKRF Sbjct: 241 FCWSIGVYGFVLWLPSILKAGAQMDMVEAGWLSALPYLAAVIGMLLVSWGSDKLQKRKRF 300 Query: 301 VWPPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGA 360 VWPPLLIA++AFYGSY LG EHFWWSYTLLVIAGACMYAPYGPFFAI+PE+LP+NVAGGA Sbjct: 301 VWPPLLIASIAFYGSYALGAEHFWWSYTLLVIAGACMYAPYGPFFAIIPEILPANVAGGA 360 Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQARRQ 419 MALINSMGALGSF GS+LVGYLN TG PGASYL M GAL+++V LT L P R + Sbjct: 361 MALINSMGALGSFGGSYLVGYLNSSTGSPGASYLLMSGALMLSVVLTVFLKPGASDRER 419 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: 883 Number of extensions: 32 Number of successful extensions: 1 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: 430 Length adjustment: 32 Effective length of query: 393 Effective length of database: 398 Effective search space: 156414 Effective search space used: 156414 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