Align histidine permease (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 377 bits (969), Expect = e-109 Identities = 193/447 (43%), Positives = 280/447 (62%), Gaps = 13/447 (2%) Query: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 L+RGL RHI+ +ALG AIGTGLF GSA ++ AGP+++L Y IGG F++MR LGEM Sbjct: 11 LQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIMRQLGEMI 70 Query: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 V PVAGSF +A Y G AGF+ GW Y V+VGMA++TA G Y+ FW+PEV W Sbjct: 71 VEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWAT 130 Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187 ++ +NL NVK FGE EFW +++KVAAIV MIL G ++ +S G+ IS Sbjct: 131 AAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLL---VSGKGGEQASIS 187 Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 NLW+ GGF PNG G++ + A++MF+FGG+E++G+TA EA +P+ V+P+AIN V RIL+ Sbjct: 188 NLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRILI 247 Query: 248 FYVLTMLVLMSIFPWQQI---------GSQGSPFVQIFDKLGISSAATILNIVVITAAIS 298 FY+ + VL++++PW + GSPFVQIF +G +AA +LN VV+TAA+S Sbjct: 248 FYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAALS 307 Query: 299 AINSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENV 358 NS ++ RM++GLA+QG AP+ ++ GVP + V V ++ LL V +NYL P+ Sbjct: 308 VYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQGA 367 Query: 359 FLLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVF 418 L+ S+A A V W MI + RR+M +Q + F ++P + +AF+ + Sbjct: 368 LELLMSLAVAALVINWAMISLAHLKFRRAM-QQQGVEPSFKAFWFPLSNYLCLAFVAGIL 426 Query: 419 GVLGYFPDTQAALIVGVVWIVLLVLAY 445 ++ + P + ++ VW+ L L Y Sbjct: 427 IIMLWLPGIRMSVFAIPVWVGFLWLCY 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: 666 Number of extensions: 31 Number of successful extensions: 3 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: 464 Length adjustment: 33 Effective length of query: 435 Effective length of database: 431 Effective search space: 187485 Effective search space used: 187485 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