Align KguT (characterized, see rationale)
to candidate Pf6N2E2_628 2-ketogluconate transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_628 Length = 432 Score = 699 bits (1803), Expect = 0.0 Identities = 339/417 (81%), Positives = 365/417 (87%) Query: 1 MQIDRLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFL 60 MQ LA RRWWYIMPIVFITYSLAYLDRANYGFAAASGMA DL ITP LSSLLGALFFL Sbjct: 1 MQTLNLATRRWWYIMPIVFITYSLAYLDRANYGFAAASGMAKDLMITPGLSSLLGALFFL 60 Query: 61 GYFFFQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVM 120 GYFFFQVPGAIYA+K SVKKLIFVSLILWG LATLTG+V + LI IRF+LGVVEAAVM Sbjct: 61 GYFFFQVPGAIYAQKHSVKKLIFVSLILWGSLATLTGVVSNAYWLIVIRFMLGVVEAAVM 120 Query: 121 PAMLIYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVL 180 PAML+YLCHWFTRAERSRANTFLILGNPVT+LWMSVVSGYLV+ FDWRWMFIIEGLPAVL Sbjct: 121 PAMLVYLCHWFTRAERSRANTFLILGNPVTMLWMSVVSGYLVQQFDWRWMFIIEGLPAVL 180 Query: 181 WAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQY 240 WAFIWWRL DDRP QA WL QEK L ALAAEQ GIK VKNY EAFRSPKVIIL+LQ+ Sbjct: 181 WAFIWWRLADDRPSQAKWLSDQEKHDLESALAAEQVGIKAVKNYAEAFRSPKVIILALQF 240 Query: 241 FCWSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRF 300 FCWSIGVYGFVLWLPSILK +++V AGWLS++PYL AV+ ML VSWASD+ QKRKRF Sbjct: 241 FCWSIGVYGFVLWLPSILKAGLQMNMVEAGWLSSLPYLAAVIGMLVVSWASDKAQKRKRF 300 Query: 301 VWPPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGA 360 VWPPLL+A++AFY SY+LG EHFWWSY+LLV+AGACMYAPYGPFFAIVPE+LP+NVAGGA Sbjct: 301 VWPPLLVASIAFYASYLLGPEHFWWSYSLLVVAGACMYAPYGPFFAIVPEILPANVAGGA 360 Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQAR 417 MALINSMGALGSF GS+LVGYLNG TG PG S+L M GALLVAV LT L P R Sbjct: 361 MALINSMGALGSFGGSYLVGYLNGSTGSPGMSFLLMSGALLVAVVLTLALKPGASDR 417 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: 886 Number of extensions: 37 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: 432 Length adjustment: 32 Effective length of query: 393 Effective length of database: 400 Effective search space: 157200 Effective search space used: 157200 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