Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate GFF84 Psest_0084 TRAP transporter, 4TM/12TM fusion protein
Query= uniprot:E4PQE4 (729 letters) >FitnessBrowser__psRCH2:GFF84 Length = 674 Score = 362 bits (928), Expect = e-104 Identities = 218/562 (38%), Positives = 312/562 (55%), Gaps = 55/562 (9%) Query: 219 LIMELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQV-YTDAGILGPT 277 L+ E RRV G+AL II +FLAY G YLPG L + G + + +Q+ + G+ G Sbjct: 114 LVFEAARRVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTP 173 Query: 278 TAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTS 337 T VS+TYI LFI+F +FL+ + + F +FA G GGPAKVS+ +S LMG I G+ Sbjct: 174 TYVSATYIFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSG 233 Query: 338 AGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTE 397 NVV+TG TIPLMK+ GY AG VEA +S G QIMPP+MGA AFIMAE +P+ E Sbjct: 234 VANVVTTGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVE 293 Query: 398 IAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQ-CYLFVPIIILIVA 456 IA AA+IPA+LYF SV++MV EA + G++G+ +DE P +K+ YL +P+++L+ Sbjct: 294 IAKAALIPALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWL 353 Query: 457 LFMGYSVIRAGTLATVSAAVV------------------SWLSPN-------KMGLRHI- 490 LF G + + AGT+ A+V W++ ++G+ I Sbjct: 354 LFSGRTPMFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIF 413 Query: 491 -----------------------LQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARF 527 L AL + A+ + + CA GVI+GV+SLTGV + F Sbjct: 414 GVIAALVAVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTF 473 Query: 528 SVLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFF 587 + +L V + L+L+ M ++LGMG+PT Y + +S+ AP L+ LG+ + +H F Sbjct: 474 AGYILAVGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMF 533 Query: 588 VFYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEA 647 VFYF +++ +TPPVALA +AAA I+ ++ S+ + RI IA FIVPFM YN AL+M+ Sbjct: 534 VFYFGIMADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQG 593 Query: 648 G-WFEIARALVTATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGI 706 G W L A F V + G+ A W ++L AAA M+ +D G Sbjct: 594 GDWGATLYMLFKAAFAVGLWGAVFTGYLQRPMALW-EKVLAFAAAASMVLAMPISDEIGF 652 Query: 707 ALAVLAFV--IQKQRKTRLATA 726 AL L + I + R+ ATA Sbjct: 653 ALGALFLIQHIWRARRAEPATA 674 Lambda K H 0.327 0.139 0.410 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: 1249 Number of extensions: 67 Number of successful extensions: 5 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: 729 Length of database: 674 Length adjustment: 39 Effective length of query: 690 Effective length of database: 635 Effective search space: 438150 Effective search space used: 438150 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: 54 (25.4 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