Align TRAP transporter (characterized, see rationale)
to candidate GFF1092 HP15_1070 TRAP-type uncharacterized transport system, fused permease component
Query= uniprot:A8LI82 (743 letters) >FitnessBrowser__Marino:GFF1092 Length = 867 Score = 216 bits (550), Expect = 4e-60 Identities = 115/290 (39%), Positives = 174/290 (60%), Gaps = 7/290 (2%) Query: 185 DLVLAICGVAVATYLITIYGTLMRNSTGTPFAPIGISI-AAVAGTALIMELTRRVAGMAL 243 D +LA+ A+YL Y L P API + A+ G L++E TRR G+ L Sbjct: 102 DWILALVAAFCASYLYVFYEELSTR----PGAPITQDLWVALIGLVLLLEATRRSLGLPL 157 Query: 244 IVIAGIFLAYVFVGQYLPGFLNAPAVTWQRFFSQVYTDA-GILGPTTAVSSTYIILFIIF 302 ++A +F+ Y G Y+P + V+ + S + G+ G VS++++ LF++F Sbjct: 158 TIVAAVFITYSIAGPYMPDVIAHKGVSLSKLASHQWLGTEGVFGVALGVSTSFVFLFVLF 217 Query: 303 AAFLQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTIPL 362 A L+ + G+YF+ A+A G RGGPAK A+ +SGL G+I+G+S NVV TG+ TIPL Sbjct: 218 GALLERAGAGNYFIKVAYAMLGHMRGGPAKAAVVSSGLSGVISGSSIANVVTTGTFTIPL 277 Query: 363 MKKVGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFV 422 MK+VG+ AGAVE AAST GQ+ PPIMGA AF+M E GI Y E+ AI+PA++ +V Sbjct: 278 MKRVGFPATKAGAVEVAASTNGQLTPPIMGAAAFLMVEYVGISYLEVIKHAILPAMISYV 337 Query: 423 SVYFMVDLEAAKLGMRGMSRDELPKF-NKMVRQVYLFLPIIILIYALFMG 471 ++ ++V LEA KL M+G+ R P +++ V + + + +L A++ G Sbjct: 338 ALIYIVHLEACKLNMQGIERLNKPTLAQRLLNWVVILIGLSVLTLAVYYG 387 Score = 152 bits (384), Expect = 7e-41 Identities = 93/268 (34%), Positives = 143/268 (53%), Gaps = 26/268 (9%) Query: 444 ELPKFNKMVRQ-VYLFLPIIILIYAL----------------FMGYSVIRAGTLATVAAA 486 ELP V+ +Y LP+++L++ L FM + V+ L Sbjct: 435 ELPPVGPTVKTGLYFLLPVVVLVWCLTVERFSPQLSAFWATLFMIFIVVTQRPLKAFFYK 494 Query: 487 VVSWFTPFRMGPRSIAKAFEIAGTMSVQIIAVCACAGIIVGVISLTGVGARFSAVLLGIA 546 ++ F+ G +A + V I A AGI+VG ++LTG+G + + ++ Sbjct: 495 HGNFLGEFKDGVFDLAHSLATGARNMVGIGVATATAGIVVGTVTLTGIGLVMTEFVEFLS 554 Query: 547 DTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLG------IPLLTAHFFVF 600 + LL L F I+++LGMG+PTTA Y V ++++AP +V LG +PL+ H FVF Sbjct: 555 GGNLLLMLIFTAIISLILGMGLPTTANYIVVSTLMAPVIVTLGAQNGLIVPLIAVHLFVF 614 Query: 601 YFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMDGT- 659 YF +L+ TPPV LA+YAAA ISGA+P+ T + F I I+PFMF +N+ +L+ G Sbjct: 615 YFGILADDTPPVGLAAYAAAAISGADPIRTGIQGFTYDIRTAILPFMFIFNTQLLLIGLT 674 Query: 660 -WFEVLRAGATAVVGVFFLSSGVQG-WF 685 WF++L +AV + S+ QG WF Sbjct: 675 GWFDLLVTIFSAVTAMLVFSAATQGFWF 702 Lambda K H 0.327 0.140 0.419 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: 1658 Number of extensions: 98 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 2 Length of query: 743 Length of database: 867 Length adjustment: 41 Effective length of query: 702 Effective length of database: 826 Effective search space: 579852 Effective search space used: 579852 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: 55 (25.8 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