Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease
Query= uniprot:A0A2Z5MFR8 (461 letters) >NCBI__GCF_000691145.1:WP_008347408.1 Length = 448 Score = 359 bits (921), Expect = e-103 Identities = 178/450 (39%), Positives = 275/450 (61%), Gaps = 5/450 (1%) Query: 5 LQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQ 64 + Q LKR L NRH+QLIA+GG IGTGLFLGS +Q AGPS+I Y I G+ F +MR Sbjct: 1 MAQQELKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRA 60 Query: 65 LGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGV 124 LGE++ + S + A Y G + F++GW YW +++ +MA++ AVG YV YW+ + Sbjct: 61 LGELLLSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWFD-I 119 Query: 125 PTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGH---GGP 181 P W+ A++C + NL VK +GE EFWFA+IKV+ ++ +I G LL+ G GP Sbjct: 120 PQWIPAIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGP 179 Query: 182 QASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVI 241 +++NLWSHGG FP+G G +++F++ G+EL+G++AAE PQK+IP A+N++ Sbjct: 180 -VTVTNLWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIP 238 Query: 242 YRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNS 301 RIL FY+ ++ VLL + PW E++A SPFV F IG + A ++N VVLT+A S NS Sbjct: 239 LRILFFYVGAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNS 298 Query: 302 GVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLL 361 G+++ SR+LY L+ Q P + ++++ VP A+ +S + +++ LIP +A G++ Sbjct: 299 GMFSTSRILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPEQAFGIV 358 Query: 362 MALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAM 421 + + W++I + HLK ++ + FK+ + P N L A ILVI+ Sbjct: 359 TTISAICFIWVWSIILICHLKYKKTRPELHKASTFKAPFTPFVNIAVLVLFAAILVIMLF 418 Query: 422 TPGLSVSVLLVPLWLVVMWAGYAFKRRRAA 451 ++LL P+W ++ YA K+RR+A Sbjct: 419 ADATRPALLLTPVWFGFLFLIYARKKRRSA 448 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: 486 Number of extensions: 24 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: 448 Length adjustment: 33 Effective length of query: 428 Effective length of database: 415 Effective search space: 177620 Effective search space used: 177620 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 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