Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate WP_010961821.1 MCA_RS12765 carbon starvation protein A
Query= SwissProt::P39396 (716 letters) >NCBI__GCF_000008325.1:WP_010961821.1 Length = 691 Score = 696 bits (1797), Expect = 0.0 Identities = 345/672 (51%), Positives = 467/672 (69%), Gaps = 24/672 (3%) Query: 1 MDTKKIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQ 60 M ++K+ + W + ++GA L +AL RGE +++LW V A+V VY + YR+YS ++A Sbjct: 1 MPSRKLTVVLTWSAVALLGASALGGIALNRGESVNSLWFVTAAVCVYALGYRFYSAFVAT 60 Query: 61 KVMKLDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTL 120 +V+ LD RATPA NDG ++VPT+R+V+FGHHFAAIAG GPL+GP LAAQ GYLPGTL Sbjct: 61 RVLLLDAGRATPAERFNDGRDFVPTHRWVVFGHHFAAIAGPGPLIGPTLAAQFGYLPGTL 120 Query: 121 WLLAGVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVL 180 W+L G V G VQDF+VL S RR+G SLG+M ++E+GP+ G+ AL G IMII++AVL Sbjct: 121 WILIGAVFGGCVQDFVVLVCSIRRDGRSLGQMARDELGPIGGSAALVGVMAIMIILIAVL 180 Query: 181 ALIVVKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGV 240 L+VV A+ SPW TV +T+PIA+ +G+YMR IRPGRV E ++IG+ LL+ S+ GG Sbjct: 181 GLVVVNAMKHSPWATSTVAATIPIAVLIGLYMREIRPGRVIEATLIGVTLLILSVAGGGW 240 Query: 241 IAHDPYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGI 300 I H P + T+ +I Y F +A+LPVWL+LAPRDYL+TF+K+G I LA+ I Sbjct: 241 IDHHPAIRTWFDYDAPTLALMIIAYGFAAAVLPVWLLLAPRDYLSTFMKLGTIAALAVAI 300 Query: 301 VVLNPELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANET 360 ++L+P+++MPA+T +IDGTGP++ G LFPF+FITIACGA+SGFHALISSGTTPKLLANE Sbjct: 301 LILHPDIRMPALTAFIDGTGPIFGGKLFPFVFITIACGAISGFHALISSGTTPKLLANEA 360 Query: 361 DARFIGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPII 420 DARFIGYGAM+MESFVAIMA++AA++++PG+YFA+N+P +G Sbjct: 361 DARFIGYGAMMMESFVAIMAMIAATVLDPGIYFAINSPAGVVG----------------- 403 Query: 421 MAQLKDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKV 480 A A AT+SSWGF + Q+ A+++GE S+ R GGAP+LAVG+A +F Sbjct: 404 -----KEAADAVATISSWGFPVDVGQMATLAREMGEASLFARTGGAPSLAVGMASLFASA 458 Query: 481 LPMADMGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGT 540 + WYHF I+FEALFILT LDAGTR RFMLQD+LGN+ P L +T + + Sbjct: 459 FGDGLLALWYHFAIMFEALFILTTLDAGTRVARFMLQDMLGNWHPVLGRTGWYPGVLFSS 518 Query: 541 AGCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVT 600 A V WGY LY G +DPLGG+ SLWPLFGI+NQMLAA+AL + T +L+K + Y W+T Sbjct: 519 ALVVAGWGYFLYMGTIDPLGGINSLWPLFGIANQMLAAIALCVATTILVKTGKASYAWIT 578 Query: 601 VVPAVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLTAQQIANMNHIVVN 660 +P WL++ T+ A KLFS ++ GF A +K+A G L+A Q A ++ N Sbjct: 579 ALPLSWLIVVTSSAAWEKLFSPELRV-GFLAHARDLGDKLAAGL-LSADQAAKAPQLIFN 636 Query: 661 NYTNAGLSILFL 672 +Y +A L+ +F+ Sbjct: 637 DYLDATLTAVFM 648 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: 1350 Number of extensions: 62 Number of successful extensions: 2 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 24 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