Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate WP_099093436.1 AU252_RS08100 amino acid permease
Query= uniprot:A0A0C4YP23 (465 letters) >NCBI__GCF_001484605.1:WP_099093436.1 Length = 469 Score = 377 bits (969), Expect = e-109 Identities = 193/441 (43%), Positives = 281/441 (63%), Gaps = 5/441 (1%) Query: 13 LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72 + RGL RHI+ +ALG AIGTGLF G A I+ AGP+VLL Y + G F +MR LGEM Sbjct: 1 MNRGLNVRHIRFMALGSAIGTGLFYGSASAIQKAGPAVLLAYIIGGAAVFMVMRALGEMA 60 Query: 73 VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132 V PV+GSF +A++Y G AGF++GW Y +V++A+++A IY+ +W+P + W Sbjct: 61 VRHPVSGSFGQYASRYLGPLAGFVTGWTYVFEMAIVAIADVTAFSIYMGFWFPQVDRWIW 120 Query: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTAGPQASVS--- 189 L + A+NL SVK FGE+EFWFS++KV+AI+ MIV G ++A G ++V+ Sbjct: 121 ILAIICFLAALNLLSVKVFGELEFWFSLIKVVAIIAMIVGGAAIIAFGFQAAGSTVAPGL 180 Query: 190 -NLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRIL 248 NL +HGG FPNG GL+ + AV+MF+FGG+E +GITA EA +P+K IPKA N V R+L Sbjct: 181 GNLVEHGGLFPNGFEGLLASFAVVMFAFGGIETLGITAGEAADPKKVIPKAVNTVPVRVL 240 Query: 249 IFYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGVYC 308 +FYV LGVL+SL+PW ++ + GSPFV IF + +LNAVV+TAALS NS ++ Sbjct: 241 LFYVLTLGVLMSLFPWNEIGSNGSPFVQIFSGLGIPAAPHILNAVVITAALSAINSDIFG 300 Query: 309 NSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMGLV 368 R+LFGL+ QG+AP KV++ G+P + + A VV+N +P + F L+ + Sbjct: 301 AGRILFGLSGQGHAPAVFGKVSRHGVPWMTVVMMAGILLVGVVLNAVIPEDVFILIASIA 360 Query: 369 VSALIINWAMISIIHLKFRRD-KRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMYLTPG 427 A + W MI H+ +R+ R A + F S +P + + +AF+A ++ V+ Sbjct: 361 TFATVWVWVMILASHVAMKREIARKALPASEFPSPWWPAASVLTIAFMALVIAVLGAFED 420 Query: 428 LRISVYLIPAWLAVLGLSYRL 448 R+++Y+ AWL +L L+YRL Sbjct: 421 TRVALYVGAAWLGLLVLAYRL 441 Lambda K H 0.326 0.140 0.426 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: 604 Number of extensions: 42 Number of successful extensions: 3 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: 465 Length of database: 469 Length adjustment: 33 Effective length of query: 432 Effective length of database: 436 Effective search space: 188352 Effective search space used: 188352 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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