Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= uniprot:Q4KIP0 (466 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 785 bits (2028), Expect = 0.0 Identities = 387/445 (86%), Positives = 413/445 (92%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 69 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 70 Query: 70 VEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWPEIPTWVS 129 VEEPVAGSFSHFAHKYWGGY GFLAGWNYWVLYVLVGMAELTAVGKY+QFWWP+IPTWVS Sbjct: 71 VEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTWVS 130 Query: 130 AAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYMLFSGSGGSQASVSNLW 189 A VFFV VNLIN +NVKFFGE EFWFAIIKVVAIVGMIVLGCY+LFSG+GG QASVSNLW Sbjct: 131 ALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGGPQASVSNLW 190 Query: 190 SHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVYRVLIFYV 249 SHGGFFPNGG GLLM+MAFIMFSFGGLELVGITAAEA+EPRKVIPKAINQVVYR+LIFYV Sbjct: 191 SHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRILIFYV 250 Query: 250 GALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLTAALSVYN 309 GAL VLLSLYPWD+LL +L A GDAYS SPFV+IFSLIG+D AA ILNFVVLTAALSVYN Sbjct: 251 GALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLTAALSVYN 310 Query: 310 SGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLAPHEALEL 369 SGVYCNSRML+GLAEQGDAPK+LMKLNKQGVPI AL ISAL+T+LCV+VNY+AP ALEL Sbjct: 311 SGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVAPQSALEL 370 Query: 370 LFALVVAALMINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAFMVMIVGVMW 429 LFALVVA+LMINWALIS+TH++FRKAM EQGV PSFK FW P SNYLCLAFMVMI+ VM Sbjct: 371 LFALVVASLMINWALISITHIKFRKAMGEQGVTPSFKTFWFPFSNYLCLAFMVMIISVML 430 Query: 430 MIPGIRASVYAIPVWVLVIWGFYLL 454 IPGI SVYA+PVWV +I+ Y L Sbjct: 431 AIPGISESVYAMPVWVGIIYVAYRL 455 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: 880 Number of extensions: 39 Number of successful extensions: 1 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: 467 Length adjustment: 33 Effective length of query: 433 Effective length of database: 434 Effective search space: 187922 Effective search space used: 187922 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