Alignments for a candidate for btsT in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for btsT in Klebsiella michiganensis M5al

Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate BWI76_RS07775 BWI76_RS07775 carbon starvation protein A

Query= SwissProt::P39396
         (716 letters)



>FitnessBrowser__Koxy:BWI76_RS07775
          Length = 701

 Score =  865 bits (2236), Expect = 0.0
 Identities = 431/700 (61%), Positives = 541/700 (77%), Gaps = 19/700 (2%)

Query: 8   KHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMKLDP 67
           K++ W +L +IGAF L  +AL RGE I+ALWIVVA+V VYL+AYR+Y LYIA+ V+ +DP
Sbjct: 6   KYLIWTLLSVIGAFALGYIALNRGEQINALWIVVAAVCVYLIAYRFYGLYIAKNVLAVDP 65

Query: 68  TRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLAGVV 127
           TR TPAV +NDGL+YVPT++ VLFGHHFAAIAGAGPLVGPVLAAQMGYLPG +W+LAGVV
Sbjct: 66  TRMTPAVRHNDGLDYVPTDKKVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGMIWILAGVV 125

Query: 128 LAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIVVKA 187
           LAGAVQDFMVLF+S+RR+G SLGE++KEEMGP  G +AL  CF+IM+IILAVLA+IVVKA
Sbjct: 126 LAGAVQDFMVLFVSTRRDGRSLGELVKEEMGPTAGVLALVACFMIMVIILAVLAMIVVKA 185

Query: 188 LAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHDPYW 247
           L  SPWG +TV  T+P+A+FMGIY+R++RPGR+GEVSVIG+V+LV +I  GG +A  P W
Sbjct: 186 LTHSPWGTYTVAFTIPLAIFMGIYIRYLRPGRIGEVSVIGLVMLVFAIISGGWVAESPTW 245

Query: 248 GPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLNPEL 307
            P   +    +T+ L+GY F++A+LPVWL+LAPRDYL+TFLKIG IVGLA+GI+++ P L
Sbjct: 246 APWFDYTGVQLTWILVGYGFIAAVLPVWLLLAPRDYLSTFLKIGTIVGLAIGILIMRPTL 305

Query: 308 KMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARFIGY 367
            MPA+T++IDGTGP+W G+LFPFLFITIACGAVSGFHALI+SGTTPK+LANE  A FIGY
Sbjct: 306 TMPALTKFIDGTGPVWSGSLFPFLFITIACGAVSGFHALIASGTTPKMLANEGQACFIGY 365

Query: 368 GAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQLKDV 427
           G MLMESFVAIMALVAA II+PG+YFAMN+P A L              AP   A + DV
Sbjct: 366 GGMLMESFVAIMALVAACIIDPGVYFAMNSPMAVL--------------AP---AGVTDV 408

Query: 428 TAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVL-PMADM 486
            A AA  VSSWGF ++P+ + Q A ++GE S+++RAGGAPTLAVG+A++ H  L  + D+
Sbjct: 409 VASAAQVVSSWGFTVTPDTLNQIAHEVGEQSIISRAGGAPTLAVGMAYILHGSLGGLMDV 468

Query: 487 GFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGCVGL 546
            FWYHF ILFEALFILTA+DAGTR+ RFMLQDLLG   P LK+T SL A ++ TA CV  
Sbjct: 469 SFWYHFAILFEALFILTAVDAGTRAARFMLQDLLGVISPGLKQTSSLPANLLATALCVLA 528

Query: 547 WGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVPAVW 606
           WGY L+QGVVDPLGG+ +LWPLFGI+NQMLA +AL+L  VVL KMKR +Y WV ++P  W
Sbjct: 529 WGYFLHQGVVDPLGGINTLWPLFGIANQMLAGMALMLCAVVLFKMKRQRYAWVALLPTSW 588

Query: 607 LLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLTAQQIANMNHIVVNNYTNAG 666
           LLICT  A   K FST+ ++ GF  +A++++  I +G        + +  +V NN  +AG
Sbjct: 589 LLICTLTAGWQKSFSTDTKV-GFLAIANKFQAMIDSGNIPPQYTESQLAQLVFNNRLDAG 647

Query: 667 LSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIP 706
           L+I F++VV  +  +  KT LA    DK T KETPY  +P
Sbjct: 648 LTIFFMVVVVVLALFSIKTALAALKEDKPTAKETPYQAMP 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: 1461
Number of extensions: 66
Number of successful extensions: 4
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: 701
Length adjustment: 39
Effective length of query: 677
Effective length of database: 662
Effective search space:   448174
Effective search space used:   448174
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources