Align histidine permease (characterized)
to candidate GFF4342 PS417_22235 aromatic amino acid transporter
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__WCS417:GFF4342 Length = 473 Score = 381 bits (978), Expect = e-110 Identities = 194/465 (41%), Positives = 283/465 (60%), Gaps = 13/465 (2%) Query: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 LKRGL RHI+ +ALG AIGTGLF GSA ++ AGP+++L Y I G FM+MR LGEM Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMI 70 Query: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 V PVAGSF +A Y G AGF+ GW ++VGM+++TA G Y+ +W+PE+ W+ Sbjct: 71 VEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYWWPEIPTWVS 130 Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187 ++ +NL NVKVFGE EFW +++KV AIV MI G +++ G G ++ Sbjct: 131 AAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTG---GPQASVT 187 Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 NLW GGF P+G+GGL+ + A++MF+FGG+E++G TA EA P+ V+P+AIN V RIL+ Sbjct: 188 NLWEHGGFFPHGVGGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPKAINQVIYRILI 247 Query: 248 FYVLTMLVLMSIFPWQQI---------GSQGSPFVQIFDKLGISSAATILNIVVITAAIS 298 FY+ ++VL+S+ PW + GSPFVQ+F LG +AA ILN VV+TAA+S Sbjct: 248 FYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAALS 307 Query: 299 AINSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENV 358 NS + RM+ G+A+QG APK A + + GVP +++ + L+ VL+NYLIP++ Sbjct: 308 VYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVAVLMNYLIPQHA 367 Query: 359 FLLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVF 418 L+ S+ V W MI F+ R+ M L F ++PY +AF++F+ Sbjct: 368 LELLMSLVVATLVINWAMISFSHFKFRQHMNRTGQVPL-FKALWYPYGNYVCLAFVVFIL 426 Query: 419 GVLGYFPDTQAALIVGVVWIVLLVLAYLMWVKPAAGQAALVARDP 463 ++ P Q ++ VW++ + + Y + K +A QA A P Sbjct: 427 VIMLMIPGIQVSVFAIPVWVMFMAVCYGIKNKRSAQQALAPAASP 471 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: 655 Number of extensions: 38 Number of successful extensions: 4 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: 473 Length adjustment: 33 Effective length of query: 435 Effective length of database: 440 Effective search space: 191400 Effective search space used: 191400 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