Align Peptide transporter CstA; Carbon starvation protein A (characterized)
to candidate BWI76_RS07775 BWI76_RS07775 carbon starvation protein A
Query= SwissProt::P15078 (701 letters) >FitnessBrowser__Koxy:BWI76_RS07775 Length = 701 Score = 1318 bits (3410), Expect = 0.0 Identities = 650/701 (92%), Positives = 685/701 (97%) Query: 1 MNKSGKYLVWTVLSVMGAFALGYIALNRGEQINALWIVVASVCIYLIAYRFYGLYIAKNV 60 MN SGKYL+WT+LSV+GAFALGYIALNRGEQINALWIVVA+VC+YLIAYRFYGLYIAKNV Sbjct: 1 MNNSGKYLIWTLLSVIGAFALGYIALNRGEQINALWIVVAAVCVYLIAYRFYGLYIAKNV 60 Query: 61 LAVDPTRMTPAVRHNDGLDYVPTDKKVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGMIWL 120 LAVDPTRMTPAVRHNDGLDYVPTDKKVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGMIW+ Sbjct: 61 LAVDPTRMTPAVRHNDGLDYVPTDKKVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGMIWI 120 Query: 121 LAGVVLAGAVQDFMVLFVSTRRDGRSLGELVKEEMGPTAGVIALVACFMIMVIILAVLAM 180 LAGVVLAGAVQDFMVLFVSTRRDGRSLGELVKEEMGPTAGV+ALVACFMIMVIILAVLAM Sbjct: 121 LAGVVLAGAVQDFMVLFVSTRRDGRSLGELVKEEMGPTAGVLALVACFMIMVIILAVLAM 180 Query: 181 IVVKALTHSPWGTYTVAFTIPLALFMGIYLRYLRPGRIGEVSVIGLVFLIFAIISGGWVA 240 IVVKALTHSPWGTYTVAFTIPLA+FMGIY+RYLRPGRIGEVSVIGLV L+FAIISGGWVA Sbjct: 181 IVVKALTHSPWGTYTVAFTIPLAIFMGIYIRYLRPGRIGEVSVIGLVMLVFAIISGGWVA 240 Query: 241 ESPTWAPYFDFTGVQLTWMLVGYGFVAAVLPVWLLLAPRDYLSTFLKIGTIVGLAVGILI 300 ESPTWAP+FD+TGVQLTW+LVGYGF+AAVLPVWLLLAPRDYLSTFLKIGTIVGLA+GILI Sbjct: 241 ESPTWAPWFDYTGVQLTWILVGYGFIAAVLPVWLLLAPRDYLSTFLKIGTIVGLAIGILI 300 Query: 301 MRPTLTMPALTKFVDGTGPVWTGNLFPFLFITIACGAVSGFHALISSGTTPKMLANEGQA 360 MRPTLTMPALTKF+DGTGPVW+G+LFPFLFITIACGAVSGFHALI+SGTTPKMLANEGQA Sbjct: 301 MRPTLTMPALTKFIDGTGPVWSGSLFPFLFITIACGAVSGFHALIASGTTPKMLANEGQA 360 Query: 361 CFIGYGGMLMESFVAIMALVSACIIDPGVYFAMNSPMAVLAPAGTADVVASAAQVVSSWG 420 CFIGYGGMLMESFVAIMALV+ACIIDPGVYFAMNSPMAVLAPAG DVVASAAQVVSSWG Sbjct: 361 CFIGYGGMLMESFVAIMALVAACIIDPGVYFAMNSPMAVLAPAGVTDVVASAAQVVSSWG 420 Query: 421 FSITPDTLNQIASEVGEQSIISRAGGAPTLAVGMAYILHGALGGMMDVAFWYHFAILFEA 480 F++TPDTLNQIA EVGEQSIISRAGGAPTLAVGMAYILHG+LGG+MDV+FWYHFAILFEA Sbjct: 421 FTVTPDTLNQIAHEVGEQSIISRAGGAPTLAVGMAYILHGSLGGLMDVSFWYHFAILFEA 480 Query: 481 LFILTAVDAGTRAARFMLQDLLGVVSPGLKRTDSLPANLLATALCVLAWGYFLHQGVVDP 540 LFILTAVDAGTRAARFMLQDLLGV+SPGLK+T SLPANLLATALCVLAWGYFLHQGVVDP Sbjct: 481 LFILTAVDAGTRAARFMLQDLLGVISPGLKQTSSLPANLLATALCVLAWGYFLHQGVVDP 540 Query: 541 LGGINTLWPLFGIANQMLAGMALMLCAVVLFKMKRQRYAWVALVPTAWLLICTLTAGWQK 600 LGGINTLWPLFGIANQMLAGMALMLCAVVLFKMKRQRYAWVAL+PT+WLLICTLTAGWQK Sbjct: 541 LGGINTLWPLFGIANQMLAGMALMLCAVVLFKMKRQRYAWVALLPTSWLLICTLTAGWQK 600 Query: 601 AFSPDAKVGFLAIANKFQAMIDSGNIPSQYTESQLAQLVFNNRLDAGLTIFFMVVVVVLA 660 +FS D KVGFLAIANKFQAMIDSGNIP QYTESQLAQLVFNNRLDAGLTIFFMVVVVVLA Sbjct: 601 SFSTDTKVGFLAIANKFQAMIDSGNIPPQYTESQLAQLVFNNRLDAGLTIFFMVVVVVLA 660 Query: 661 LFSIKTALAALKDPKPTAKETPYEPMPENVEEIVAQAKGAH 701 LFSIKTALAALK+ KPTAKETPY+ MP + + +V QAK AH Sbjct: 661 LFSIKTALAALKEDKPTAKETPYQAMPADADSLVTQAKRAH 701 Lambda K H 0.327 0.140 0.435 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: 1740 Number of extensions: 69 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: 701 Length of database: 701 Length adjustment: 39 Effective length of query: 662 Effective length of database: 662 Effective search space: 438244 Effective search space used: 438244 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