Align KguT (characterized, see rationale)
to candidate H281DRAFT_05212 H281DRAFT_05212 Sugar phosphate permease
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__Burk376:H281DRAFT_05212 Length = 429 Score = 608 bits (1567), Expect = e-178 Identities = 295/410 (71%), Positives = 336/410 (81%) Query: 6 LAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFF 65 LA RRWW IMPIVFITYSLAYLDRANYGFAAA+G+ DL I+ LSSL+GALFFLGYFFF Sbjct: 5 LAIRRWWTIMPIVFITYSLAYLDRANYGFAAAAGINQDLGISKGLSSLIGALFFLGYFFF 64 Query: 66 QVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLI 125 Q+PGAIYAE+RSVKKL+F SL+LWGG A LTGMV ++ L+ IRF+LGVVEAAVMPAMLI Sbjct: 65 QIPGAIYAERRSVKKLVFWSLVLWGGCAALTGMVSNIPSLMVIRFVLGVVEAAVMPAMLI 124 Query: 126 YLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFIW 185 ++ +WFT++ERSRANTFLILGNPVT+LWMSVVSGYLV F WR MFI EG+PA+LWA W Sbjct: 125 FISNWFTKSERSRANTFLILGNPVTVLWMSVVSGYLVHSFGWRNMFIAEGIPAILWAVCW 184 Query: 186 WRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWSI 245 W +V D+P+Q SWL Q+K L + L AEQ IKPV+NY EAFRS VI L QYFCWSI Sbjct: 185 WFIVQDKPQQVSWLTQQQKDDLAQTLRAEQAAIKPVRNYSEAFRSSAVIKLCAQYFCWSI 244 Query: 246 GVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPL 305 GVYGFVLWLPSILK ++L +V GWLSA+PYL A +AML SWASD++ +RK FVWP L Sbjct: 245 GVYGFVLWLPSILKNGSSLGMVETGWLSALPYLAATIAMLAASWASDKLNRRKVFVWPFL 304 Query: 306 LIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALIN 365 LI A+AF SY LG+ HFW SY LVIAGA MYAPYGPFFAIVPELLP NVAGGAMALIN Sbjct: 305 LIGAIAFAASYALGSTHFWLSYASLVIAGAAMYAPYGPFFAIVPELLPKNVAGGAMALIN 364 Query: 366 SMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQ 415 SMGALGSF GS++VGYLNG TG P ASY FM AL+ AV LT ++ P QQ Sbjct: 365 SMGALGSFVGSYVVGYLNGATGSPAASYAFMSVALIAAVILTLIVKPQQQ 414 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: 806 Number of extensions: 35 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: 429 Length adjustment: 32 Effective length of query: 393 Effective length of database: 397 Effective search space: 156021 Effective search space used: 156021 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