Align general amino acid permease AGP1 (characterized)
to candidate 14398 b0260 putative amino acid/amine transport protein (VIMSS)
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__Keio:14398 Length = 467 Score = 229 bits (583), Expect = 3e-64 Identities = 139/446 (31%), Positives = 221/446 (49%), Gaps = 22/446 (4%) Query: 109 TGHKSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCI 168 T ++ LK+T++ RH++M++LG IGTGL G + G AG L+ Y I +++ + Sbjct: 3 TTQQNAPLKRTMKTRHLIMLSLGGVIGTGLFFNTGYIISTTGAAGTLLAYLIGALVVWLV 62 Query: 169 IQACGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYW 228 +Q GE+++ TG ++ Y + + G+ VAW+Y L W A ++YW Sbjct: 63 MQCLGELSVAMPE-TGAFHVYAARYLGPATGYTVAWLYWLTWTVALGSSFTAAGFCMQYW 121 Query: 229 TTSVNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGN 288 V V+ ++F ++ +N+ R +AE EF+F+ K++ + F ILG GA Sbjct: 122 FPQVPVWVWCVVFCAIIFGLNVISTRFFAEGEFWFSLVKVVTIIAFIILG------GAAI 175 Query: 289 DGFIGGKYWHDPGAFNGKHAIDRFKG----VAATLVTAAFAFGGSEFIAITTAEQSNPRK 344 GFI + + A F + T+V FAF G+E I I E NPRK Sbjct: 176 FGFIPMQDGSPAPGLSNITAEGWFPHGGLPILMTMVAVNFAFSGTELIGIAAGETENPRK 235 Query: 345 AIPGAAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVV 404 IP A + I R++ F+ T+ +L L+P G + SP+V+ G+ Sbjct: 236 VIPVAIRTTIARLIIFFIGTVFVLAALIPMQQV--------GVEKSPFVLVFEKVGIPYA 287 Query: 405 PHFINAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFA 464 N VIL ++LS ANS Y+S R+ +LS + P F+ + + G PL A+ VS L Sbjct: 288 ADIFNFVILTAILSAANSGLYASGRMLWSLSNERTLPACFARVTKNGVPLTALSVSMLGG 347 Query: 465 VIAFCAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQT 524 V+A ++ + VF L AISG + + W +IC SH FRR QG++L EL +++ Sbjct: 348 VLALFSSVVAPDTVFVALSAISGFAVVAVWLSICASHFVFRRRHLQQGKALSELHYRAP- 406 Query: 525 GVWGSAYACIMMILILIAQFWVAIAP 550 W + +L L+A +A P Sbjct: 407 --WYPLVPVLGFVLCLVACVGLAFDP 430 Lambda K H 0.324 0.138 0.424 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: 710 Number of extensions: 36 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: 633 Length of database: 467 Length adjustment: 35 Effective length of query: 598 Effective length of database: 432 Effective search space: 258336 Effective search space used: 258336 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 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