Align histidine permease (characterized)
to candidate PfGW456L13_4400 Aromatic amino acid transport protein AroP
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4400 Length = 473 Score = 381 bits (979), Expect = e-110 Identities = 199/469 (42%), Positives = 286/469 (60%), Gaps = 14/469 (2%) Query: 2 QKPANG-LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM 60 Q P +G LKRGL RHI+ +ALG AIGTGLF GSA ++ AGP+++L Y I G FM+M Sbjct: 4 QNPQSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIM 63 Query: 61 RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFP 120 R LGEM V +PVAGSF +A Y G AGF+ GW ++VGM+++TA G Y+ +W P Sbjct: 64 RQLGEMIVEDPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAP 123 Query: 121 EVSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAP 180 ++ W ++ +NL NVKVFGE EFW +++KV AIV MI G +++ G Sbjct: 124 DIPTWASAAAFFVLINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGNG--- 180 Query: 181 GQVTDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINA 240 G +SNLW+ GGF PNG+ GL+ + A +MF+FGG+E++G TA EA P+ V+P+AIN Sbjct: 181 GPQAAVSNLWSHGGFFPNGVTGLVMAMAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 Query: 241 VPLRILLFYVLTMLVLMSIFPWQQI---------GSQGSPFVQIFDKLGISSAATILNIV 291 V RIL+FY+ +++L+S+ PW + GSPFVQ+F LG ++AA ILN V Sbjct: 241 VIYRILIFYIGALVILLSLTPWDSLLTTLNASGDSYSGSPFVQVFSMLGSNTAAHILNFV 300 Query: 292 VITAAISAINSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLN 351 V+TAA+S NS + RM+ G+A+QG APK A + + GVP +++ + L+ VLLN Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAVTLIAVLLN 360 Query: 352 YLIPENVFLLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAI 411 YLIP + L+ S+ V W MI ++ R+ M + L F ++PY + Sbjct: 361 YLIPHSALELLMSLVVATLVINWAMISYSHFKFRQHMNKTKQTPL-FKALWYPYGNYICL 419 Query: 412 AFMLFVFGVLGYFPDTQAALIVGVVWIVLLVLAYLMWVKPAAGQAALVA 460 AF+LF+ GV+ P Q ++ VW+V + + Y + K +A A VA Sbjct: 420 AFVLFILGVMLLIPGIQTSVYAIPVWLVFMWVCYGIKNKRSAQHALQVA 468 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: 673 Number of extensions: 43 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