Align TRAP transporter (characterized, see rationale)
to candidate WP_007151845.1 MDG893_RS01040 TRAP transporter permease
Query= uniprot:A8LI82 (743 letters) >NCBI__GCF_000170835.1:WP_007151845.1 Length = 865 Score = 222 bits (565), Expect = 7e-62 Identities = 120/309 (38%), Positives = 179/309 (57%), Gaps = 12/309 (3%) Query: 185 DLVLAICGVAVATYLITIYGTLMRNSTGTPFAPIGIS-IAAVAGTALIMELTRRVAGMAL 243 D +LA+ A+YL Y L P +PI I A+ G L++E TRR G+ L Sbjct: 101 DWILALAAAFAASYLYLFYDQLATR----PGSPITQDLIIALGGLVLLLEATRRALGLPL 156 Query: 244 IVIAGIFLAYVFVGQYLPGFLNAPAVTWQRFFSQVYTDA-GILGPTTAVSSTYIILFIIF 302 V+AG+FL Y G Y+P ++ + + S ++ G+ G VS++++ LF++F Sbjct: 157 TVVAGVFLIYALAGPYMPDVISHKGASLSKLSSHMWLGTEGVFGVALGVSTSFVFLFVLF 216 Query: 303 AAFLQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTIPL 362 A L+ + G+YF+ A+A G RGGPAK A+ +SGL G+I+G+S NVV TG+ TIPL Sbjct: 217 GALLERAGAGNYFIQVAYAMLGHMRGGPAKAAVVSSGLSGVISGSSIANVVTTGTFTIPL 276 Query: 363 MKKVGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFV 422 MK+VG+ AGAVE AAST GQ+ PPIMGA AF+M E GI Y E+ AI+PA++ +V Sbjct: 277 MKRVGFPATKAGAVEVAASTNGQLTPPIMGAAAFLMVEYVGISYLEVIKHAILPALISYV 336 Query: 423 SVYFMVDLEAAKLGMRGMSRDELPKF-NKMVRQVYLFLPIIILIYALFMGYSVIRAGTLA 481 ++ ++V LEA KL M+G+ R P +M+ V + + + + + ++ G G L Sbjct: 337 ALIYIVHLEACKLKMKGIERPNRPTLAQRMLNWVVILIGLSAITFIVYYG-----IGWLK 391 Query: 482 TVAAAVVSW 490 V W Sbjct: 392 VVLGEAAVW 400 Score = 156 bits (394), Expect = 5e-42 Identities = 96/277 (34%), Positives = 146/277 (52%), Gaps = 25/277 (9%) Query: 441 SRDELPKFNKMVRQ-VYLFLPIIILIYAL----------------FMGYSVIRAGTLATV 483 S D LP+ V+ +Y LP+++L++ L FM + VI L Sbjct: 431 SMDTLPEVGPTVKTGLYFLLPVVVLVWCLTVERFSPQLSAFWATVFMIFIVITQQPLKAF 490 Query: 484 AAAVVSWFTPFRMGPRSIAKAFEIAGTMSVQIIAVCACAGIIVGVISLTGVGARFSAVLL 543 ++ T + G + + G V I A AGI+VG ++LTG+G + + Sbjct: 491 FREKGNFLTETKTGFVDLTHSLVTGGRNMVGIGVATATAGIVVGTVTLTGIGLVMTQFVE 550 Query: 544 GIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLG------IPLLTAHF 597 I+ + LL L F I+++LGMG+PTTA Y V ++++AP +V LG +PL+ H Sbjct: 551 FISGGNLLLMLVFTALISLILGMGLPTTANYIVVSTLMAPVIVTLGAQNGLLVPLIAVHL 610 Query: 598 FVFYFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMD 657 FVFYF +L+ TPPV LA+YAAA ISGA+P+ T V F I I+PFMF +N+ +L+ Sbjct: 611 FVFYFGILADDTPPVGLAAYAAAAISGADPIRTGVQGFTYDIRTAILPFMFIFNTQLLLI 670 Query: 658 GT--WFEVLRAGATAVVGVFFLSSGVQGWFMGGRAAW 692 G W ++L A+AV + S+ QG++ W Sbjct: 671 GLTGWVDLLVTIASAVTAMLVFSAATQGYWFTKSYKW 707 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: 1633 Number of extensions: 95 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 743 Length of database: 865 Length adjustment: 41 Effective length of query: 702 Effective length of database: 824 Effective search space: 578448 Effective search space used: 578448 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 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