Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate N515DRAFT_4411 N515DRAFT_4411 carbon starvation protein
Query= SwissProt::P39396 (716 letters) >FitnessBrowser__Dyella79:N515DRAFT_4411 Length = 691 Score = 791 bits (2042), Expect = 0.0 Identities = 387/698 (55%), Positives = 517/698 (74%), Gaps = 28/698 (4%) Query: 10 IPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMKLDPTR 69 I W + I+GA+CL VVALRRGE I+A+W+V A+++V+++ YR+YS +I V+++DP+R Sbjct: 14 ILWAAIAIVGAWCLGVVALRRGEPINAIWLVAAAIAVFVIGYRFYSRFIDTYVLRMDPSR 73 Query: 70 ATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLAGVVLA 129 ATPAV+ NDGL+YVPT+++V+FGHHFAAIAGAGPLVGPVLAAQMGYLPGTLW+L GVV A Sbjct: 74 ATPAVLRNDGLDYVPTDKWVVFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWILFGVVFA 133 Query: 130 GAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIVVKALA 189 GAVQDFM+L +S RR+G SLG M+++E+GPV G +A+FG ++M+I+LAVLAL+VVKAL Sbjct: 134 GAVQDFMILGLSVRRDGRSLGNMLRDELGPVAGIVAMFGVLVLMMIVLAVLALVVVKALT 193 Query: 190 ESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHDPYWGP 249 SPWG +TV T+PIAL MGIY+R+IRPG++ EVS++G++LL+ +I+ G +A P W Sbjct: 194 HSPWGTYTVACTIPIALLMGIYLRYIRPGKILEVSIVGLILLLLAIWSGAYVAASPAWAA 253 Query: 250 ALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLNPELKM 309 A F + + LI Y F +++LPVWL+LAPRDYL+TFLKIG I LAL I + P L+M Sbjct: 254 AFDFDAKALAWLLIAYGFCASVLPVWLLLAPRDYLSTFLKIGTIALLALAIFLAAPTLQM 313 Query: 310 PAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARFIGYGA 369 PA+T+++DGTGP+++G LFPFLFITIACGAVSG+H++ISSGTTPKLL+NE +AR +GYG Sbjct: 314 PALTKFVDGTGPVFQGNLFPFLFITIACGAVSGWHSIISSGTTPKLLSNEGEARMVGYGG 373 Query: 370 MLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQLKDVTA 429 MLME+FVAIMAL+AA+ + PG+YFAMN+P A +G T + Sbjct: 374 MLMEAFVAIMALIAAASMHPGVYFAMNSPAALIGTTAQS--------------------- 412 Query: 430 HAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVLP-MADMGF 488 AA +S WGFV+SP+++L TA++IGE S+L+RAGGAPTLAVG+A + H ++P M F Sbjct: 413 -AATAISQWGFVVSPDELLNTARNIGESSILSRAGGAPTLAVGMAQLLHGIIPGEGMMAF 471 Query: 489 WYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGCVGLWG 548 WYH+ ILFEALFILT +DAGTR GRFM+Q++ G LK T+S +I TA CVGLWG Sbjct: 472 WYHYAILFEALFILTTVDAGTRVGRFMIQEIAGLIHEPLKHTESWTGNLIATAICVGLWG 531 Query: 549 YLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVPAVWLL 608 Y LYQG VDPLGG+ +LWPLFGI+NQMLAAVAL+L TVV +K+KR +Y+WV +PA+WL+ Sbjct: 532 YFLYQGAVDPLGGINTLWPLFGIANQMLAAVALMLATVVTVKLKRERYVWVPGIPAIWLV 591 Query: 609 ICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVNNYTNAGL 667 +CT A KL + F A +Y A G L A+ +A M IV NNY +A L Sbjct: 592 VCTLTAGYYKLVGS----ISFTAAAQKYAAAAAEGKLLAPAKSVAEMQRIVTNNYVDAAL 647 Query: 668 SILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPI 705 + +F+++V ++ + L + T E PYV + Sbjct: 648 TGIFMLLVVTMAGFAINAILKAWRVNHPTAHEEPYVAL 685 Lambda K H 0.327 0.142 0.440 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: 1408 Number of extensions: 59 Number of successful extensions: 4 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: 716 Length of database: 691 Length adjustment: 39 Effective length of query: 677 Effective length of database: 652 Effective search space: 441404 Effective search space used: 441404 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