Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate GFF992 PS417_05030 major facilitator transporter
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__WCS417:GFF992 Length = 455 Score = 313 bits (802), Expect = 7e-90 Identities = 162/435 (37%), Positives = 259/435 (59%), Gaps = 12/435 (2%) Query: 13 ATQRSSLDAQALINDAPLSRYQWLIAIVCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQ 72 A+ R++LDA+ P+SRYQWLI ++ L++ DG D +G++ PALAQDWG++++ Sbjct: 6 ASFRAALDAR------PVSRYQWLILLLLALLLVTDGYDAQVLGYVVPALAQDWGLEKAA 59 Query: 73 LGPVMSAALGGMIIGALVSGPTADRFGRKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRF 132 GPV SA L G+ +G+L+ P ADRFG + +L +L++ T+ ++ +L +L+ RF Sbjct: 60 FGPVFSANLLGLTLGSLLVTPLADRFGVRRILLGCVLIYASLTVLMVFANSLTTLMAARF 119 Query: 133 LTGIGLGAAMPNATTLFSEYCPARIRSLLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSL 192 + GIG+G AMP+A L SEY P R+R+L+VT CG++ G A GGF+++ I FGW ++ Sbjct: 120 ICGIGMGGAMPSAMALMSEYSPPRLRTLMVTLAACGFSFGGAAGGFVAAGFIEGFGWQAV 179 Query: 193 FLLGGWAPLILMLLVIFFLPESYRFLIVKGKNTKKVRQILSRIAP-QKVQGVTEFHVPEE 251 FL GG PL+L +++ LPES L+ +++ + SR+ P + TE E Sbjct: 180 FLAGGVTPLLLFPFLVWLLPESLPRLLRDAPPYARLQNVTSRMLPGWQPPLATE---AEN 236 Query: 252 KVEAGTKKGVFGMLFSAKYVKGTVLLWVTYFMGLVMIYLLTSWLPTLMRETGASLERAAF 311 + E G+K V LF Y + T+L+W T+F+ L+++Y + SWLP+L+ E+G +L+ A Sbjct: 237 QQEQGSKLTVV-ELFRNGYARPTLLIWSTFFVSLILLYFMISWLPSLLLESGLALKEANL 295 Query: 312 LGGLFQFGGVLSALFIGWAMDRFNPN-RIIAGFYLAAGIFAVIVGQSLSNPTLLALFILC 370 + +F F G L A+ + W DR R+++G AA + +++G + NP L ++ Sbjct: 296 VTSMFLFAGTLGAIAMAWFADRLKRKVRLLSGVLAAAAVCTLLLGLNHDNPRYLVACVVA 355 Query: 371 AGIAVNGAQSSMPVLSARFYPTQCRATGVAWMSGIGRFGAVFGAWIGAVLLGNNWSFTMI 430 AG + G Q ++ ++ FYP RATG W G+GRFG++ G G++LL + I Sbjct: 356 AGFCIIGGQLTLNAFASNFYPAHVRATGTGWALGVGRFGSILGPLFGSLLLAMHIPVQQI 415 Query: 431 LSMLIIPAAAAAIAI 445 IPA AA+ I Sbjct: 416 FFFCAIPAVIAALLI 430 Lambda K H 0.328 0.141 0.438 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: 616 Number of extensions: 33 Number of successful extensions: 6 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: 457 Length of database: 455 Length adjustment: 33 Effective length of query: 424 Effective length of database: 422 Effective search space: 178928 Effective search space used: 178928 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 (21.8 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