Align histidine permease (characterized)
to candidate BWI76_RS08745 BWI76_RS08745 proline-specific permease
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__Koxy:BWI76_RS08745 Length = 459 Score = 609 bits (1571), Expect = e-179 Identities = 296/446 (66%), Positives = 356/446 (79%), Gaps = 1/446 (0%) Query: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 L RGL+ARHIRF+ALGSAIGTGLFYGSASAI+ AGPAVLLAYLIGGAAVF+VMRALGEMA Sbjct: 9 LLRGLNARHIRFIALGSAIGTGLFYGSASAIKAAGPAVLLAYLIGGAAVFIVMRALGEMA 68 Query: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 V NPV+GSF YA YLGP+AGFI GWTY FEMVIV +ADVTAFGIYMG W+P+V RWIW Sbjct: 69 VRNPVSGSFSSYARQYLGPLAGFITGWTYTFEMVIVALADVTAFGIYMGLWYPDVPRWIW 128 Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187 VL ++ +G +NLC+V+VFGEMEFWLSL+KV AI+AMI+ G I+ FG A T + Sbjct: 129 VLSIIFFIGAMNLCSVRVFGEMEFWLSLIKVVAIIAMIVAGGSIIFFGFGNA-FPATGLE 187 Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 NLW+ GGF PNG G+IAS +VMFAFGG+EIIGVTA EAK+PQ V+P+AIN +PLRI+L Sbjct: 188 NLWSHGGFAPNGWEGIIASLGIVMFAFGGVEIIGVTAAEAKNPQKVIPQAINTIPLRIVL 247 Query: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307 FYV T+ +LM+IFPW G +GSPFV IFD LGI +AATILNI+VI+A+ISAINSDIFGA Sbjct: 248 FYVCTLAILMAIFPWNSFGERGSPFVLIFDGLGIPAAATILNIIVISASISAINSDIFGA 307 Query: 308 GRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASIAT 367 GRMM+G+A++G APK F ++ NGVPWMTVVVM VALL V+LNYL+PE VF+LIAS+A Sbjct: 308 GRMMYGMAKEGLAPKSFQRIASNGVPWMTVVVMGVALLAAVVLNYLMPEQVFVLIASLAA 367 Query: 368 FATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPDT 427 FATVWVW+MIL AMRR ++AE+ + FPVP WP AP+ + FM V VLG +T Sbjct: 368 FATVWVWVMILLAHFAMRRGLSAEERGNIAFPVPLWPVAPLLTLLFMGLVIAVLGMVEET 427 Query: 428 QAALIVGVVWIVLLVLAYLMWVKPAA 453 + ALI G+VW+ LL + V+ A Sbjct: 428 RIALIAGLVWLGLLTAVWFARVRKNA 453 Lambda K H 0.329 0.142 0.441 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: 801 Number of extensions: 44 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: 468 Length of database: 459 Length adjustment: 33 Effective length of query: 435 Effective length of database: 426 Effective search space: 185310 Effective search space used: 185310 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