Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate 1937132 b3795 predicted transporter (NCBI)
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Keio:1937132 Length = 461 Score = 374 bits (960), Expect = e-108 Identities = 188/438 (42%), Positives = 285/438 (65%), Gaps = 4/438 (0%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69 L+RGL+ RHI+LIALGG IG GLF+G+AS L+ AGPS++L Y I G+ F IMR +GEM+ Sbjct: 8 LQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMRSMGEML 67 Query: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129 EPV GSF+ +A++Y F G+L+ W+YW +++ V ++E+TA+G YV +W+P + W+ Sbjct: 68 FLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPEMAQWIP 127 Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFG-GYLLVS-GHGGPQASISN 187 AL+ A + NLA V+ YGE EFWFA+IKV +I MI+ G G + G+GG SN Sbjct: 128 ALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGNGGQSIGFSN 187 Query: 188 LWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIF 247 L HGGFF G+ G T L +++ S+ G+ELIGITA EA PQ ++ AV +V++RILIF Sbjct: 188 LTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVLWRILIF 247 Query: 248 YICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANS 307 Y+ ++ V+++++PWNE+ + GSPFV+ F++IG T A ++N VVLTAALS NSG+Y+ Sbjct: 248 YVGAIFVIVTIFPWNEIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCNSGMYSCG 307 Query: 308 RMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVA 367 RMLY LA+ P A+ KV R GVP + +S +NY+IP + + Sbjct: 308 RMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYIIPNPQRVFVYVYSAS 367 Query: 368 AL--VLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMTPGL 425 L ++ W +I ++ L+ RRA AA + F+S FP +N++ +AF+ +L+ + Sbjct: 368 VLPGMVPWFVILISQLRFRRAHKAAIASHPFRSILFPWANYVTMAFLICVLIGMYFNEDT 427 Query: 426 SVSVLLVPLWLVVMWAGY 443 +S+ + ++++ + A Y Sbjct: 428 RMSLFVGIIFMLAVTAIY 445 Lambda K H 0.327 0.140 0.440 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: 568 Number of extensions: 30 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: 461 Length of database: 461 Length adjustment: 33 Effective length of query: 428 Effective length of database: 428 Effective search space: 183184 Effective search space used: 183184 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 (21.7 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