Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease
Query= uniprot:Q4KIP0 (466 letters) >NCBI__GCF_000691145.1:WP_008347408.1 Length = 448 Score = 369 bits (948), Expect = e-107 Identities = 191/462 (41%), Positives = 281/462 (60%), Gaps = 16/462 (3%) Query: 5 LKQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQ 64 + Q ELKR L NRH+QLIA+GG IGTGLFLGS ++ AGPS+I Y I G F +MR Sbjct: 1 MAQQELKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRA 60 Query: 65 LGEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWPEI 124 LGE+++ + S + A Y G + F+ GW YW +++ MA++ AVG YVQ+W+ +I Sbjct: 61 LGELLLSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF-DI 119 Query: 125 PTWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYMLFSG--SGGSQ 182 P W+ A + +++ N++ VK FGE EFWFA+IKV+ I+ +I +G +L G + Sbjct: 120 PQWIPAIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGP 179 Query: 183 ASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVY 242 +V+NLWSHGG FPNG TG L++ ++F++ G+ELVG++AAE A P+K IP AIN++ Sbjct: 180 VTVTNLWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPL 239 Query: 243 RVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLT 302 R+L FYVGA+ VLL + PW EL + S SPFVK F LIG AA ++NFVVLT Sbjct: 240 RILFFYVGAIFVLLCINPWTEL---------SASESPFVKTFGLIGIPVAAGLINFVVLT 290 Query: 303 AALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLA 362 +A S NSG++ SR+LY L+ Q P + +LNK VP AL +S ++ + L++ L Sbjct: 291 SAASACNSGMFSTSRILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLI 350 Query: 363 PHEALELLFALVVAALMINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAFMV 422 P +A ++ + + W++I + HL+++K E +FKA ++P N L Sbjct: 351 PEQAFGIVTTISAICFIWVWSIILICHLKYKKTRPELHKASTFKAPFTPFVNIAVLVLFA 410 Query: 423 MIVGVMWMIPGIRASVYAIPVWVLVIWGFYLLSRAKKASQPA 464 I+ +M R ++ PVW +GF L A+K + A Sbjct: 411 AILVIMLFADATRPALLLTPVW----FGFLFLIYARKKRRSA 448 Lambda K H 0.327 0.141 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: 626 Number of extensions: 39 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: 466 Length of database: 448 Length adjustment: 33 Effective length of query: 433 Effective length of database: 415 Effective search space: 179695 Effective search space used: 179695 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