Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_017598723.1 D471_RS33945 TRAP transporter large permease subunit
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_000341125.1:WP_017598723.1 Length = 455 Score = 154 bits (389), Expect = 9e-42 Identities = 133/425 (31%), Positives = 198/425 (46%), Gaps = 85/425 (20%) Query: 371 TGGQIMPPIMGAGAFI------MAEITGIPYTEIAIAAIIPAILYFASVYFMVDFEAAKT 424 T G ++ P++ A + M G T +AI + IL + + D E + Sbjct: 10 TRGYLIAPVVAIFALLSMGFSPMFSAMGAVVTTVAINVLTQYIL----MPWRRDEETGEL 65 Query: 425 GMRGMREDELPKLRTMMKQCYLFVPIIILIVA---LFMGYSVIRAG-------------- 467 R R+ P +R L +PII+ VA L M + AG Sbjct: 66 KTRSGRDITSPAVR-------LPLPIIVAAVAATVLVMVGQWVMAGMDRGMVALATTLLL 118 Query: 468 TLATVSAAVV--SWLSP--NKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGV 523 TLA ++ AV W +++ L L L A+ +AI IIV CA+AGVI GVI+ T + Sbjct: 119 TLAGIAVAVAFGRWRESGEDQLNLHSFLDGLVGAARLAIPIIVACASAGVIAGVITTTDL 178 Query: 524 GARFSVLLLDVA--------------ATSQLLA-----------------------LIFA 546 G + S LL +A A S +LA L + Sbjct: 179 GLKLSDGLLGIAESISSGLASLLTAVAASPVLAWTGAGADFGATAVGTLRVDLFLILFMS 238 Query: 547 MFISILLGMGMPTTAAYAVAASVVAPGLV---QLGIEP-----LTAHFFVFYFAVVSAIT 598 M ++LG+G+PTTA Y + A++ AP +V Q ++ L AH FV+YF V++ IT Sbjct: 239 MIACLILGIGLPTTANYVITATLAAPAIVAVLQGSVDERLAMLLMAHLFVYYFGVLADIT 298 Query: 599 PPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLM-EAGWFEIARALV 657 PPV LA+YAA+GISG + + T S RI IAAF++P+MF ++ LL+ E W A + Sbjct: 299 PPVCLAAYAASGISGGDPIRTGFYSVRIAIAAFVMPYMFVFSPELLLQEVNWLTGTIAAI 358 Query: 658 TATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQK 717 T G M++ G++G + +W R+ LI LL++ G L + G+ L V +K Sbjct: 359 TGVAGAVMVALGLVG-YVDRPLAWYKRVGLIVGGLLLVSGSLVANAVGLVLIVAVLGYEK 417 Query: 718 QRKTR 722 R R Sbjct: 418 LRTRR 422 Score = 37.0 bits (84), Expect = 2e-06 Identities = 77/336 (22%), Positives = 133/336 (39%), Gaps = 57/336 (16%) Query: 434 LPKLRTMM-KQCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVS---------WLSPN 483 LP LR +M + YL P++ + L MG+S + + A V+ ++ W Sbjct: 1 LPTLRRLMITRGYLIAPVVAIFALLSMGFSPMFSAMGAVVTTVAINVLTQYILMPWRRDE 60 Query: 484 KMGLRHILQALEIAS---YMAIQIIVVCAAAGVIVGVISLT------GVGARFSVLLLDV 534 + G +I S + + IIV AA V+V V G+ A + LLL + Sbjct: 61 ETGELKTRSGRDITSPAVRLPLPIIVAAVAATVLVMVGQWVMAGMDRGMVALATTLLLTL 120 Query: 535 AATSQLLA-----------LIFAMFISILLG---MGMPTTAAYA---VAASVVAPGLVQL 577 A + +A L F+ L+G + +P A A V A V+ + L Sbjct: 121 AGIAVAVAFGRWRESGEDQLNLHSFLDGLVGAARLAIPIIVACASAGVIAGVITTTDLGL 180 Query: 578 GIEPLTAHFFVFYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMF 637 + + ++++ VA + A +GA+ T+V + R+ + F++ FM Sbjct: 181 KLSDGLLGIAESISSGLASLLTAVAASPVLAWTGAGADFGATAVGTLRVDL--FLILFMS 238 Query: 638 FYNGALLMEAGWFEIARALVTATFG----VYMLSGGV------------LGWFASISASW 681 L++ G A ++TAT V +L G V ++ + A Sbjct: 239 MI-ACLILGIGLPTTANYVITATLAAPAIVAVLQGSVDERLAMLLMAHLFVYYFGVLADI 297 Query: 682 ITRLLLIAAALLMIEGG--LWTDLTGIALAVLAFVI 715 + L A A I GG + T + +A+ AFV+ Sbjct: 298 TPPVCLAAYAASGISGGDPIRTGFYSVRIAIAAFVM 333 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: 827 Number of extensions: 47 Number of successful extensions: 5 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: 455 Length adjustment: 36 Effective length of query: 693 Effective length of database: 419 Effective search space: 290367 Effective search space used: 290367 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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