Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate HSERO_RS09795 HSERO_RS09795 carbon starvation protein A
Query= SwissProt::P39396 (716 letters) >FitnessBrowser__HerbieS:HSERO_RS09795 Length = 689 Score = 860 bits (2221), Expect = 0.0 Identities = 435/703 (61%), Positives = 534/703 (75%), Gaps = 24/703 (3%) Query: 5 KIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMK 64 +I + W+ L + GA A VAL+RGE I+A+W+VVA+V VYL+AYR+YS +IA +V+ Sbjct: 3 RIVSRLGWLALALAGAGACAYVALQRGESINAVWLVVAAVCVYLIAYRFYSKFIADRVLG 62 Query: 65 LDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLA 124 LD R TPA NDGL+YVPTN+YVLFGHHFAAIAGAGPLVGPVLAAQMGYLPG LW+LA Sbjct: 63 LDGGRMTPAYKFNDGLDYVPTNKYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGMLWILA 122 Query: 125 GVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIV 184 GVV AGAVQDFMVLFIS+RR+G SLG++IK E+G VPG IALFG F+IM+IILAVLALIV Sbjct: 123 GVVFAGAVQDFMVLFISTRRDGRSLGDLIKSELGQVPGVIALFGAFMIMVIILAVLALIV 182 Query: 185 VKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHD 244 VKALAESPWG FTV +T+PIALFMG+Y R+IRPGR+GEVS IG VLL+ +I G + Sbjct: 183 VKALAESPWGSFTVAATIPIALFMGVYSRYIRPGRIGEVSWIGFVLLMLAIVGGQYVQEH 242 Query: 245 PYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLN 304 P G TF +T+ LIGY FV+++LPVWL+LAPRDYL+TFLKIG I+ LALGIV + Sbjct: 243 PALGQMFTFDGKQLTWMLIGYGFVASVLPVWLLLAPRDYLSTFLKIGTILALALGIVFIA 302 Query: 305 PELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARF 364 P LKM A+T++IDG+GP+W G+LFPFLFITIACGAVSGFHALISSGTTPKLL NE ARF Sbjct: 303 PHLKMHAVTRFIDGSGPVWSGSLFPFLFITIACGAVSGFHALISSGTTPKLLENEKHARF 362 Query: 365 IGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQL 424 IGYGAMLMESFVAIMAL+AAS IEPG+YFAMN+P A +G T N+ Sbjct: 363 IGYGAMLMESFVAIMALIAASCIEPGIYFAMNSPAALIGTTPENV--------------- 407 Query: 425 KDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVLPMA 484 A +S WGF I+PE + TA+ +GE ++++RAGGAPTLAVG+A + V A Sbjct: 408 -------AQVISQWGFHITPEMLTHTAQAVGEHTIISRAGGAPTLAVGMAQILSGVTGEA 460 Query: 485 DMGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGCV 544 M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG FIP +K+TDS VA +I T CV Sbjct: 461 MMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGAFIPPMKRTDSWVASLIATGLCV 520 Query: 545 GLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVPA 604 WGY LYQGVVDPLGG+ +LWPLFGISNQMLA +AL+L T VL KMKR ++ WVTV+P Sbjct: 521 AGWGYFLYQGVVDPLGGINTLWPLFGISNQMLAGIALILATCVLFKMKRDRFAWVTVLPT 580 Query: 605 VWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVNNYT 663 WLL CT A K+F NP++ GF AS+Y+ + G L A+ I M ++ N+Y Sbjct: 581 AWLLACTLTAGWQKVFDANPRV-GFLAHASKYQAALDEGKLLAPAKSIEQMRQVIFNDYV 639 Query: 664 NAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIP 706 +AGL+ +F++VV S++ +G +T L R++ + + KE PY +P Sbjct: 640 DAGLAAMFMLVVISVLVFGIRTVLKARSAHQPSVKEAPYETLP 682 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: 1389 Number of extensions: 55 Number of successful extensions: 3 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: 689 Length adjustment: 39 Effective length of query: 677 Effective length of database: 650 Effective search space: 440050 Effective search space used: 440050 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