Align valine/tyrosine/tryptophan amino-acid permease (characterized)
to candidate 14398 b0260 putative amino acid/amine transport protein (VIMSS)
Query= CharProtDB::CH_091631 (619 letters) >FitnessBrowser__Keio:14398 Length = 467 Score = 217 bits (553), Expect = 8e-61 Identities = 131/438 (29%), Positives = 223/438 (50%), Gaps = 32/438 (7%) Query: 84 SQEKNNLTKSIKSRHLVMISLGTGIGTGLLVGNGQVLGTAGPAGLVLGYGIASIMLYCII 143 +Q+ L +++K+RHL+M+SLG IGTGL G ++ T G AG +L Y I +++++ ++ Sbjct: 4 TQQNAPLKRTMKTRHLIMLSLGGVIGTGLFFNTGYIISTTGAAGTLLAYLIGALVVWLVM 63 Query: 144 QAAGELGLCYAGLTGNYTRYPSILVDPSLGFAVSVVYTIQWLTVLPLQLVTAAMTVKYW- 202 Q GEL + TG + Y + + P+ G+ V+ +Y + W L A ++YW Sbjct: 64 QCLGELSVAMPE-TGAFHVYAARYLGPATGYTVAWLYWLTWTVALGSSFTAAGFCMQYWF 122 Query: 203 TSVNADIFVAVVFVFVIIINLFGSRGYAEAEFIFNSCKILMVIGFVILAIIINCGGAGDR 262 V ++ V + +N+ +R +AE EF F+ K++ +I F+IL GGA Sbjct: 123 PQVPVWVWCVVFCAIIFGLNVISTRFFAEGEFWFSLVKVVTIIAFIIL------GGAAIF 176 Query: 263 RYI---------GAEYWHNPGPFAHGFKGVCTVFCYAAFSYGGIEVLLLSAAEQENPTKS 313 +I G G F HG + F++ G E++ ++A E ENP K Sbjct: 177 GFIPMQDGSPAPGLSNITAEGWFPHGGLPILMTMVAVNFAFSGTELIGIAAGETENPRKV 236 Query: 314 IPNACKKVVYRILLIYMLTTILVCFLVPYNSDELLGSSDSSGSHASPFVIAVASHGVKVV 373 IP A + + R+++ ++ T ++ L+P G SPFV+ G+ Sbjct: 237 IPVAIRTTIARLIIFFIGTVFVLAALIPMQQ---------VGVEKSPFVLVFEKVGIPYA 287 Query: 374 PHFINAVILISVISVANSSLYSGPRLLLSLAEQGVLPKCLAYVDRNGRPLLCFFVSLVFG 433 N VIL +++S ANS LY+ R+L SL+ + LP C A V +NG PL VS++ G Sbjct: 288 ADIFNFVILTAILSAANSGLYASGRMLWSLSNERTLPACFARVTKNGVPLTALSVSMLGG 347 Query: 434 CIGFVATSDAEEQVFTWLLAISSLSQLFIWMSMSLSHIRFRDAMAKQGRSMNEVGYKAQT 493 + ++ A + VF L AIS + + +W+S+ SH FR +QG++++E+ Y+A Sbjct: 348 VLALFSSVVAPDTVFVALSAISGFAVVAVWLSICASHFVFRRRHLQQGKALSELHYRA-- 405 Query: 494 GYWGSWLAVLIAIFFLVC 511 W ++ + F++C Sbjct: 406 ----PWYPLVPVLGFVLC 419 Lambda K H 0.324 0.138 0.420 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: 696 Number of extensions: 38 Number of successful extensions: 5 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: 619 Length of database: 467 Length adjustment: 35 Effective length of query: 584 Effective length of database: 432 Effective search space: 252288 Effective search space used: 252288 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: 40 (21.5 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