Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_090272364.1 BLU11_RS05175 TRAP transporter permease
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_900105005.1:WP_090272364.1 Length = 862 Score = 218 bits (555), Expect = 1e-60 Identities = 128/373 (34%), Positives = 204/373 (54%), Gaps = 35/373 (9%) Query: 162 FHQRERSVFSVPDLVLIVCSLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIM 221 F + R+ + D V+ + AAY + Y + V + A+ G L++ Sbjct: 87 FRRSPRNHVPLTDWVMALVGAFCAAYIYIFYAALAERPGSPTTTDVVV---ALVGLVLLL 143 Query: 222 ELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFS-QVYTDAGILGPTTAV 280 E TRR G L+I+ L+F+ Y AGPY+PG L + G+S+ + Q + G+ G V Sbjct: 144 EATRRALGPPLMIVALLFIIYSVAGPYMPGMLAHRGVSLTSLANHQWLSTQGVFGIALGV 203 Query: 281 SSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGN 340 S++++ LF++F + L + G+YF+ AF+ G RGGPAK ++ ASG+ G+I+G+S N Sbjct: 204 STSFVFLFVLFGSLLDKAGAGNYFIKLAFSLLGHYRGGPAKAAVAASGMTGLISGSSIAN 263 Query: 341 VVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAI 400 V+TG+ TIP+MK+VGY+ + AGAVE +AS GQIMPP+MGA AF+M E GI YTE+ Sbjct: 264 TVTTGTFTIPMMKRVGYTAEQAGAVEVSASVNGQIMPPVMGAAAFLMVEYVGISYTEVIT 323 Query: 401 AAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQCYLFVPIIILIVALFMG 460 A +PA++ + +++++V A K GM+G+ +R ++ F+ ++LI+ L Sbjct: 324 HAFLPAMISYIALFYIVHLAALKAGMQGLESSN--PVRPFARKMLGFLTGLLLIMGL--- 378 Query: 461 YSVIRAGTLATVSAAVVSWLSPNKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISL 520 +LA + WL P AL + + I AAG+ + I+L Sbjct: 379 -------SLAVYYG--LGWLKP----------ALGVYASWVI-------AAGLAIAYIAL 412 Query: 521 TGVGARFSVLLLD 533 VG+ + L LD Sbjct: 413 LRVGSHYPDLDLD 425 Score = 132 bits (333), Expect = 6e-35 Identities = 104/330 (31%), Positives = 162/330 (49%), Gaps = 32/330 (9%) Query: 398 IAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLR-TMMKQCYLFVPIIILIVA 456 +AIA I A+L S Y +D + + + M P+ R T+M + +P+I+L+ Sbjct: 405 LAIAYI--ALLRVGSHYPDLDLDDPNSPVVSM-----PQTRPTLMTGLHFILPVIVLVWC 457 Query: 457 LFMG-YSVIRAGTLATVSAAVVSW--------------LSPN-KMGLRHILQALEIASYM 500 L + S + ATV ++ L N + G + L + Sbjct: 458 LMVERLSPALSAFWATVFMTIIMLTQHPLIAMFRKERDLGRNIRRGFCDFWEGLVAGARN 517 Query: 501 AIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTT 560 I I + A AG+IVG +S TGVG + L+ ++ + LL L +S++LGMG+PTT Sbjct: 518 MIGIGIATATAGIIVGAVSQTGVGLVLADLVEVLSMGNLLLMLALTAVLSLILGMGLPTT 577 Query: 561 AAYAVAASVVAPGLVQLG-----IEPLTA-HFFVFYFAVVSAITPPVALASYAAAGISGA 614 A Y V ++++AP +V LG I PL A H FVFYF +++ +TPPV LAS+AAA ISG Sbjct: 578 ANYIVVSALLAPVIVTLGQQNGLIVPLIAVHLFVFYFGIMADVTPPVGLASFAAAAISGG 637 Query: 615 NAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARAL-VTATFGVYMLSGGVLGW 673 + + T +F + +PF+F +N LL+ F + V AT + + + GW Sbjct: 638 DPIRTGFQAFYYSLRTAALPFLFIFNTDLLLIDVSFTYGLVIFVVATVAMLIFAAATQGW 697 Query: 674 FASISASWITRLLLIAAALLMIEGGLWTDL 703 + S W LL+ A + G W D+ Sbjct: 698 MITRS-RWYESALLLLVAFTLFRPGFWMDM 726 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: 1524 Number of extensions: 90 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: 729 Length of database: 862 Length adjustment: 41 Effective length of query: 688 Effective length of database: 821 Effective search space: 564848 Effective search space used: 564848 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