Align histidine permease (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 378 bits (971), Expect = e-109 Identities = 199/449 (44%), Positives = 279/449 (62%), Gaps = 14/449 (3%) Query: 2 QKPANGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMR 61 Q L+RGL RHI+ +ALG AIGTGLF G A IQ+AGP+VLL Y I G F++MR Sbjct: 4 QSTPERLQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFLIMR 63 Query: 62 ALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPE 121 LGEM V PVAGSF +A Y AGF+ GW Y V+VGMA++TA GIY+ +W+P+ Sbjct: 64 QLGEMVVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPD 123 Query: 122 VSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPG 181 W ++ +NL VKV+GEMEFW +L+KV AIV+MI GFG L G S G Sbjct: 124 FPTWATAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMI--GFGAWLLG-SGHGG 180 Query: 182 QVTDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAV 241 ++NLW GGF PNG+ GL+ + AV+MF+FGG+E++G+TA EA +P+ +P+A N V Sbjct: 181 PDASVANLWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQV 240 Query: 242 PLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAIN 301 RIL+FY+ + VL+S++PWQ++ GSPFV IF +L ATILNIVV+TAA+S N Sbjct: 241 VYRILIFYIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYN 300 Query: 302 SDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLL 361 S ++ RM+FGLA QG AP+ +SR+GVP + V + A L VL+NYL+P F L Sbjct: 301 SCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAFGL 360 Query: 362 IASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFW-----PYAPMAAIAFMLF 416 + ++A A V W I T + R++ A + PF+ P +AF++ Sbjct: 361 LMALAVSALVINWASISITHLKFRKAKLAAGI------TPFYKSLGHPLTNYLCLAFIVL 414 Query: 417 VFGVLGYFPDTQAALIVGVVWIVLLVLAY 445 + V+ P + ++++ WI +L +A+ Sbjct: 415 ILVVMYLTPPIRISVMLIPAWIAVLWVAF 443 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: 634 Number of extensions: 29 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: 453 Length adjustment: 33 Effective length of query: 435 Effective length of database: 420 Effective search space: 182700 Effective search space used: 182700 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