Align KguT (characterized, see rationale)
to candidate PP_3377 PP_3377 2-ketogluconate transporter, putative
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__Putida:PP_3377 Length = 430 Score = 762 bits (1968), Expect = 0.0 Identities = 366/418 (87%), Positives = 390/418 (93%) Query: 1 MQIDRLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFL 60 MQ LAPRRWWYI+PIVF+TYSLAYLDRANYGFAAASGMA+DLHITP LSSLLGALFFL Sbjct: 1 MQSQSLAPRRWWYIIPIVFVTYSLAYLDRANYGFAAASGMAEDLHITPVLSSLLGALFFL 60 Query: 61 GYFFFQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVM 120 GYFFFQVPGAIYAEKRSVKKLIFV LILWGGLATLTGMV +V +LI IRFLLGVVEAAVM Sbjct: 61 GYFFFQVPGAIYAEKRSVKKLIFVCLILWGGLATLTGMVSNVYMLIGIRFLLGVVEAAVM 120 Query: 121 PAMLIYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVL 180 PAML+YLCHWFTRAERSRANTFL+LGNPVTILWMSVVSGYL+KH+DWRWMFIIEGLPAV+ Sbjct: 121 PAMLVYLCHWFTRAERSRANTFLMLGNPVTILWMSVVSGYLIKHYDWRWMFIIEGLPAVI 180 Query: 181 WAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQY 240 WAF WWRLVDDRP Q +WL QEK AL +ALAAEQQGIKPVKNYREAFRSP+VIIL+LQY Sbjct: 181 WAFFWWRLVDDRPAQVAWLSEQEKAALAQALAAEQQGIKPVKNYREAFRSPQVIILALQY 240 Query: 241 FCWSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRF 300 FCWSIGVYGFVLWLPSILKQAA +DIV AGWL++VPYL AVLAM+GVSWASDR+QKRKRF Sbjct: 241 FCWSIGVYGFVLWLPSILKQAANVDIVQAGWLASVPYLAAVLAMVGVSWASDRLQKRKRF 300 Query: 301 VWPPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGA 360 VWPPLLIAALAFYGSY LG+EHFW SY LLV+AGACMYAPYGPFFAIVPE+LP+NVAGGA Sbjct: 301 VWPPLLIAALAFYGSYALGSEHFWLSYALLVVAGACMYAPYGPFFAIVPEILPANVAGGA 360 Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQARR 418 MALINSMGALGSF GSWLVGYLNG TGGPGASYLFMCGALL AVALTA LN SQ + R Sbjct: 361 MALINSMGALGSFGGSWLVGYLNGATGGPGASYLFMCGALLTAVALTAALNTSQTSGR 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: 896 Number of extensions: 41 Number of successful extensions: 2 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