Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate PP_4641 PP_4641 putative transporter
Query= SwissProt::P39396 (716 letters) >FitnessBrowser__Putida:PP_4641 Length = 688 Score = 999 bits (2582), Expect = 0.0 Identities = 491/708 (69%), Positives = 590/708 (83%), Gaps = 25/708 (3%) Query: 2 DTKKIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQK 61 + + +HIPW+ L +IGA L VVALRRGE I+ALWIVVA+V++YLVAYRYYSL+IA K Sbjct: 3 NNNSLLRHIPWLALAVIGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIATK 62 Query: 62 VMKLDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLW 121 VM+LDP RATPAV+NNDGL+YVPTN+++LFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLW Sbjct: 63 VMQLDPRRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLW 122 Query: 122 LLAGVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLA 181 L+AGVVLAGAVQDFMVLF+S+RRNG SLG+M++EEMG +PGTIALFGCFLIMIIILAVLA Sbjct: 123 LIAGVVLAGAVQDFMVLFLSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLA 182 Query: 182 LIVVKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVI 241 LIVVKALAESPWG+FTV +T+PIA+FMGIYMR+IRPGR+GE+SV+G+VLL+ASI+ GGVI Sbjct: 183 LIVVKALAESPWGMFTVMATIPIAMFMGIYMRYIRPGRIGEISVVGVVLLLASIWLGGVI 242 Query: 242 AHDPYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIV 301 A DP WGPA TF IT+ L+GY FV+A+LPVWL+LAPRDYL+TFLKIG I+GLA+GI+ Sbjct: 243 AADPVWGPAFTFTGVQITWMLVGYGFVAAVLPVWLVLAPRDYLSTFLKIGTILGLAIGIL 302 Query: 302 VLNPELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETD 361 ++ PELKMPA+TQ+ DGTGP+WKG LFPFLFITIACGAVSGFHALISSGTTPKLL NET+ Sbjct: 303 IIAPELKMPALTQFTDGTGPVWKGTLFPFLFITIACGAVSGFHALISSGTTPKLLDNETN 362 Query: 362 ARFIGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIM 421 AR+IGYG MLMESFVAIMA+VAAS+IEPG+YFAMN+P A +G + Sbjct: 363 ARYIGYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAVVGTDV--------------- 407 Query: 422 AQLKDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVL 481 A A TVSSWGF+I+PEQ+ A+DIGE ++L RAGGAPTLAVGIA + H+VL Sbjct: 408 -------ASVAQTVSSWGFLITPEQLEAVARDIGEHTILARAGGAPTLAVGIAQILHQVL 460 Query: 482 PMAD-MGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGT 540 P + M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P LK+T+S A ++ T Sbjct: 461 PGENTMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPALKRTESWGANLLAT 520 Query: 541 AGCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVT 600 AGCV LWGYLLYQGV+DPLGG+ +LWPLFGISNQMLA +AL+LGTVVLIKMKR +YIWVT Sbjct: 521 AGCVALWGYLLYQGVIDPLGGINTLWPLFGISNQMLAGIALMLGTVVLIKMKRQRYIWVT 580 Query: 601 VVPAVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVV 659 ++PAVWLLICTT A +KLF NP + GF +A +Y + G L A+ I M H++ Sbjct: 581 LLPAVWLLICTTAAGLIKLFDPNPAV-GFLALAKKYSTALDAGQVLAPAKDIGQMQHVIF 639 Query: 660 NNYTNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPE 707 N YTNAGL+ILFL+VV+SI+F+ K A +R+DKETP+ +P+ Sbjct: 640 NAYTNAGLTILFLLVVFSILFFAIKVGYAALGRKERSDKETPFQALPD 687 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: 1561 Number of extensions: 74 Number of successful extensions: 6 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: 688 Length adjustment: 39 Effective length of query: 677 Effective length of database: 649 Effective search space: 439373 Effective search space used: 439373 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