Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_050776516.1 MDG893_RS16430 TRAP transporter permease
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_000170835.1:WP_050776516.1 Length = 660 Score = 353 bits (906), Expect = e-101 Identities = 206/553 (37%), Positives = 321/553 (58%), Gaps = 49/553 (8%) Query: 217 TALIMELTRRVAGMALVIIGLVFLAYVFAGP---------YLPGFLGYPGLSVQRFFSQV 267 T ++E +RR G L +IG++ + Y +G +LPG L + G S+ R +Q+ Sbjct: 108 TITLLEASRRAVGTGLTVIGVIAILYAMSGQRGPLSELGEWLPGILNHRGYSLDRIGAQL 167 Query: 268 YT-DAGILGPTTAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFA 326 Y GI G V++T++ +F++F A L+ + G +F++ AFAA GR RGGPAK ++ A Sbjct: 168 YLGQEGIFGLPLGVAATFVFIFVLFGAMLEVTGAGRFFIDLAFAATGRQRGGPAKAAVLA 227 Query: 327 SGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFI 386 S MG I+G++ NVV+TG+ TIPLMKK+G+ AG +EAAASTGGQIMPP+MGAGAF+ Sbjct: 228 SASMGSISGSAIANVVTTGAFTIPLMKKLGFRPAQAGGIEAAASTGGQIMPPLMGAGAFL 287 Query: 387 MAEITGIPYTEIAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQ-CY 445 +AE T +PY +I ++ PA+LYFA+VY +V A K GM+G+ +LP+LR +M Y Sbjct: 288 IAEYTRVPYLDIVKVSVFPALLYFATVYLLVHICAVKQGMKGLPASDLPQLREVMAYGWY 347 Query: 446 LFVPIIILIVALFMGYSVIRAGTLATVSAAVVSWL-----------SPNKMG------LR 488 +PII+L+ L MG S +R G A V ++ L + N++G LR Sbjct: 348 FLLPIIMLVYLLVMGISPMRVGFYAVVGIIGIAGLNGLYLAYKQGRADNQLGKALTDALR 407 Query: 489 H----ILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLALI 544 +LQ LE+ + A+ + + CA AG++V V+ LTG+G +FS +++ A + L+AL Sbjct: 408 EGVVKLLQGLELGARNAVPVSIACAIAGIVVAVVGLTGLGLKFSSMMIAFADGNILMALF 467 Query: 545 FAMFISILLGMGMPTTAAYAVAASVVAPGLV-QLGIEPLTAHFFVFYFAVVSAITPPVAL 603 + S++LG+G+P TA+Y V +V P L + GI L AH VF+++ S +TPPVAL Sbjct: 468 LVVIASLILGLGLPVTASYIVLIVLVGPALTNEFGIPLLVAHLLVFWYSQDSNVTPPVAL 527 Query: 604 ASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAG------WFEIARALV 657 A++A A I+G+ METSV +++ +++P +N +++E G W L Sbjct: 528 AAFAGAAIAGSKTMETSVQAWKFAKGLYLIPLFMVFN-PVIIEGGPLPLVLWNGFIAILA 586 Query: 658 TATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQK 717 A F + + G+ + W+ RL L A + + L ++ G+ +A+LA + Sbjct: 587 LAAF-----AAALEGFLFTHMKPWM-RLALSGAVIAIFYPDLQVEVAGV-VAMLALLAMN 639 Query: 718 --QRKTRLATAGA 728 R+ L AGA Sbjct: 640 YWHRRRELHGAGA 652 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: 1281 Number of extensions: 82 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 729 Length of database: 660 Length adjustment: 39 Effective length of query: 690 Effective length of database: 621 Effective search space: 428490 Effective search space used: 428490 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 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