Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate RR42_RS20515 RR42_RS20515 carbon starvation protein A
Query= SwissProt::P39396 (716 letters) >FitnessBrowser__Cup4G11:RR42_RS20515 Length = 690 Score = 902 bits (2332), Expect = 0.0 Identities = 457/704 (64%), Positives = 553/704 (78%), Gaps = 25/704 (3%) Query: 5 KIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMK 64 +I +H+ W+ + I+GAF A VAL RGE +SALWIVVA++ +YL+AYRYYS +IA+KVM+ Sbjct: 3 RIGQHLVWLAVAILGAFAFATVALSRGEAVSALWIVVAAICIYLIAYRYYSKFIAEKVMQ 62 Query: 65 LDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLA 124 LDP R TPA +NDGL+YVPTN+ VLFGHHFAAIAGAGPLVGPVLAAQMGY+PG LW+LA Sbjct: 63 LDPKRMTPAWRHNDGLDYVPTNKAVLFGHHFAAIAGAGPLVGPVLAAQMGYMPGMLWILA 122 Query: 125 GVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIV 184 GVV AGAVQDFMVLFIS+RR+G SLG++IK EMG VPG IALFGCF+IMIIILAVLALIV Sbjct: 123 GVVFAGAVQDFMVLFISTRRDGRSLGDLIKSEMGTVPGMIALFGCFMIMIIILAVLALIV 182 Query: 185 VKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHD 244 VKALA SPWG FTV T+PIALFMGIY R+IRPGR+GEVSVIG VLL+ +I G + Sbjct: 183 VKALAGSPWGTFTVGVTIPIALFMGIYTRYIRPGRIGEVSVIGFVLLMLAIIGGQYVHES 242 Query: 245 PYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLN 304 P T+ +T+ LI Y F++A+LPVWL+LAPRDYL+TFLKIG I+ LA+GI+++ Sbjct: 243 AVLAPLFTYDGKALTWMLIIYGFIAAVLPVWLLLAPRDYLSTFLKIGTIIALAIGILIVA 302 Query: 305 PELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARF 364 PELKMPA TQ+ G GP+W G LFPFLFITIACGAVSGFHALISSGTTPKLL +E RF Sbjct: 303 PELKMPAFTQFAKGGGPVWSGNLFPFLFITIACGAVSGFHALISSGTTPKLLESEAHMRF 362 Query: 365 IGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQL 424 IGYGAML ESFVAIMALVAAS+IEPG+YFAMN+P A +G +P +AQ+ Sbjct: 363 IGYGAMLAESFVAIMALVAASVIEPGVYFAMNSPAAVIG------------TSPESVAQV 410 Query: 425 KDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVL-PM 483 VS WGFVI+P+ ++QTAKD+GE S+++RAGGAPTLAVGIAH+ H+V+ Sbjct: 411 ----------VSGWGFVITPDVLIQTAKDVGENSIISRAGGAPTLAVGIAHILHQVVGGQ 460 Query: 484 ADMGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGC 543 A M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P ++TDSL A +I TA Sbjct: 461 AMMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPSFRRTDSLPANLIATALT 520 Query: 544 VGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVP 603 V WGY LYQGVVDPLGG+ +LWPLFGISNQMLAAVALVLGT VL+KMKR QY WVT+VP Sbjct: 521 VSFWGYFLYQGVVDPLGGINTLWPLFGISNQMLAAVALVLGTCVLVKMKRGQYAWVTLVP 580 Query: 604 AVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVNNY 662 +WLLICT A KLF +P++ F A+++ + IA G L A+ + M+ IV N+Y Sbjct: 581 TIWLLICTLTAGWQKLFDADPKV-SFLTHAAKFSDAIAQGKVLAPAKSMEQMHRIVFNDY 639 Query: 663 TNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIP 706 +AGL LF+ VV SI+FYGFKT + R ++ TD+ETP+ P+P Sbjct: 640 LDAGLCALFMFVVLSIVFYGFKTAMKARAENRPTDRETPFEPMP 683 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: 1446 Number of extensions: 73 Number of successful extensions: 7 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: 690 Length adjustment: 39 Effective length of query: 677 Effective length of database: 651 Effective search space: 440727 Effective search space used: 440727 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