Align KguT (characterized, see rationale)
to candidate BWI76_RS12915 BWI76_RS12915 4-hydroxyphenylacetate permease
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__Koxy:BWI76_RS12915 Length = 457 Score = 210 bits (534), Expect = 8e-59 Identities = 128/412 (31%), Positives = 214/412 (51%), Gaps = 18/412 (4%) Query: 14 IMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIYA 73 ++ +F+ + ++LDR N GFA + M+ DL +T + L LF++ Y F VP I Sbjct: 28 LVAFLFVLFVFSFLDRINIGFAGLT-MSQDLGLTSTMFGLAATLFYVTYVLFGVPSNIML 86 Query: 74 EKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFTR 133 + ++ I V +++WG +T T S L A+R ++GV EA +P +L+YL WF Sbjct: 87 SRVGARRWIAVIMVVWGVASTCTLFATSAGTLYALRMIVGVAEAGFVPGILLYLTWWFPS 146 Query: 134 AERSRANTFLILGNPVTILWMSVVSGYL------VKHFDWRWMFIIEGLPAVLWAFIWWR 187 R+RAN ++ P+T+++ S++SGY+ + W+W+F++EGLP+V+ + W Sbjct: 147 WYRARANALFMIAMPLTMMFGSMLSGYILALDGVMNLRGWQWLFLLEGLPSVILGVVTWF 206 Query: 188 LVDDRPEQASWLKAQEKTALREALAAEQQ------GIKPVKNYREAFRSPKVIILSLQYF 241 +DD+P A WL A EK L+ + +++ +PV +RE F +P V++ L YF Sbjct: 207 YLDDKPADAKWLNADEKQTLQRMMESDRSVNRKMLTRRPVSLWREVF-TPVVVLYILAYF 265 Query: 242 CWSIGVYGFVLWLPSILKQ-AAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRF 300 C + + +W P ILK A+ +T G L+A+P ++ M+ S SDR+++RKR Sbjct: 266 CLTNSLSAINIWTPQILKSFNASSSNITVGLLAAIPQFCTIVVMMWWSKRSDRLKERKRH 325 Query: 301 VWPPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGA 360 P L +A + + + T H + L++A A + F+ + Sbjct: 326 TIYPYLFSAAGWLLTSL--TAHPLIQLSGLIMASAGAFTAMTLFWTTPDRAISVGAQAVV 383 Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNP 412 +A I+ G +GS L+G ++ +TG A FM G LLV AL V P Sbjct: 384 LATISGAGNIGSGLSPLLIGVMHDMTGNFNAGLWFMAG-LLVIGALVLVYIP 434 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: 597 Number of extensions: 39 Number of successful extensions: 6 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: 457 Length adjustment: 32 Effective length of query: 393 Effective length of database: 425 Effective search space: 167025 Effective search space used: 167025 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