Align histidine permease (characterized)
to candidate BWI76_RS04870 BWI76_RS04870 aromatic amino acid transporter AroP
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__Koxy:BWI76_RS04870 Length = 455 Score = 389 bits (998), Expect = e-112 Identities = 204/452 (45%), Positives = 285/452 (63%), Gaps = 4/452 (0%) Query: 2 QKPANGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMR 61 Q+ + LKRGL RHI+ +ALG AIGTGLF GSAS IQ AGP ++L Y I G F++MR Sbjct: 4 QQHGDRLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQNAGPGIILGYAIAGFIAFLIMR 63 Query: 62 ALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPE 121 LGEM V PVAGSF +A Y G AGF GW Y V+V MA++TA G Y+ FW+PE Sbjct: 64 QLGEMVVEEPVAGSFSHFAYKYWGGFAGFASGWNYWVLYVLVAMAELTAVGKYVQFWWPE 123 Query: 122 VSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPG 181 + W+ + +NL NVKVFGEMEFW +++KV A+VAMIL G G +LF + P Sbjct: 124 IPTWVSAAIFFIAINAINLTNVKVFGEMEFWFAIIKVVAVVAMILFG-GWLLFSGNGGP- 181 Query: 182 QVTDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAV 241 Q T + NLW QGGF+P+G GL+ A++MF+FGG+E++G+TA EA +P+ +P+A N V Sbjct: 182 QAT-VRNLWEQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQV 240 Query: 242 PLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAIN 301 RIL+FYV ++ VL+S+ PW ++ + SPFV IF +LG + A LNIVV+TAA+S N Sbjct: 241 IYRILIFYVGSLAVLLSLLPWSRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYN 300 Query: 302 SDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLL 361 S ++ RM+FGLAQQG+APK + + GVP T++V ++ L VL+NY PE+ F L Sbjct: 301 SCVYCNSRMLFGLAQQGNAPKALMSVDKRGVPVNTILVSALVTALCVLINYFAPESAFGL 360 Query: 362 IASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVL 421 + ++ A V W MI + RR+ + V +FP +P + + FM V ++ Sbjct: 361 LMALVVSALVINWAMISLAHIKFRRAKQQQGVV-TRFPALLYPLSNWICLLFMAGVLVIM 419 Query: 422 GYFPDTQAALIVGVVWIVLLVLAYLMWVKPAA 453 P ++ + VWI +L + YL K A+ Sbjct: 420 LMTPGMAISVYLIPVWIAVLGVGYLFKQKTAS 451 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: 680 Number of extensions: 40 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: 455 Length adjustment: 33 Effective length of query: 435 Effective length of database: 422 Effective search space: 183570 Effective search space used: 183570 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