Alignments for a candidate for cstA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for cstA in Klebsiella michiganensis M5al

Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate BWI76_RS03820 BWI76_RS03820 carbon starvation protein A

Query= SwissProt::P39396
         (716 letters)



>FitnessBrowser__Koxy:BWI76_RS03820
          Length = 716

 Score = 1371 bits (3548), Expect = 0.0
 Identities = 674/716 (94%), Positives = 704/716 (98%)

Query: 1   MDTKKIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQ 60
           MDTKK+FKHIPWVILGIIGAFCL+VVALRRGEH+SALWIVVASVSVYLVAYRYYSLYIAQ
Sbjct: 1   MDTKKLFKHIPWVILGIIGAFCLSVVALRRGEHVSALWIVVASVSVYLVAYRYYSLYIAQ 60

Query: 61  KVMKLDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTL 120
           KVMKLDPTR+TPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTL
Sbjct: 61  KVMKLDPTRSTPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTL 120

Query: 121 WLLAGVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVL 180
           WLLAGVVLAGAVQDFMVLFISSRRNGASLGEMIK+EMGPVPG+IALFGCFLIMIIILAVL
Sbjct: 121 WLLAGVVLAGAVQDFMVLFISSRRNGASLGEMIKQEMGPVPGSIALFGCFLIMIIILAVL 180

Query: 181 ALIVVKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGV 240
           ALIVVKALAESPWGVFTVCSTVPIALFMGIYMRF+RPGRVGEVSVIGIVLLVASIYFGG+
Sbjct: 181 ALIVVKALAESPWGVFTVCSTVPIALFMGIYMRFLRPGRVGEVSVIGIVLLVASIYFGGI 240

Query: 241 IAHDPYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGI 300
           IAHDPYWGPALTFKDTTITF LIGYAF+SALLPVWLILAPRDYLATFLKIGVIVGLALGI
Sbjct: 241 IAHDPYWGPALTFKDTTITFTLIGYAFISALLPVWLILAPRDYLATFLKIGVIVGLALGI 300

Query: 301 VVLNPELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANET 360
           V+LNP+LKMPA+TQYIDGTGPLWKGALFPFLFITIACGAVSGFHALI+SGTTPKLLANET
Sbjct: 301 VILNPDLKMPAVTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALIASGTTPKLLANET 360

Query: 361 DARFIGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPII 420
           DARFIGYGAMLMESFVA+MALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENA +I
Sbjct: 361 DARFIGYGAMLMESFVAVMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAALI 420

Query: 421 MAQLKDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKV 480
            AQL+DVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHK+
Sbjct: 421 AAQLRDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKI 480

Query: 481 LPMADMGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGT 540
           +PMADMGFWYHFGILFEALFILTALDAGTR+GRFMLQDLLGNF+PFLKKTDSLVAGIIGT
Sbjct: 481 IPMADMGFWYHFGILFEALFILTALDAGTRAGRFMLQDLLGNFVPFLKKTDSLVAGIIGT 540

Query: 541 AGCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVT 600
           AGCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVL+KM+RT+YIWVT
Sbjct: 541 AGCVGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLVKMQRTKYIWVT 600

Query: 601 VVPAVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLTAQQIANMNHIVVN 660
           V+PA WLL+CTTWALGLKLFSTNPQMEGFF+MA QYKEKIA G +LTAQQIANMNHIVVN
Sbjct: 601 VIPAAWLLLCTTWALGLKLFSTNPQMEGFFFMAQQYKEKIAAGGELTAQQIANMNHIVVN 660

Query: 661 NYTNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPEGGVKISSHH 716
           NYTNAGLSILFL+VVYSIIFYG KTWL VRN+  RTDKETPYVP+PEGGVK SSHH
Sbjct: 661 NYTNAGLSILFLVVVYSIIFYGIKTWLNVRNNKVRTDKETPYVPVPEGGVKTSSHH 716


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: 1803
Number of extensions: 64
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: 716
Length adjustment: 40
Effective length of query: 676
Effective length of database: 676
Effective search space:   456976
Effective search space used:   456976
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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