Alignments for a candidate for xacF in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacF in Mesorhizobium ciceri WSM1271

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate YP_004139899.1 Mesci_0678 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= reanno::Smeli:SM_b20891
         (477 letters)



>NCBI__GCF_000185905.1:YP_004139899.1
          Length = 505

 Score =  313 bits (802), Expect = 9e-90
 Identities = 192/480 (40%), Positives = 259/480 (53%), Gaps = 38/480 (7%)

Query: 13  VGGDGVANINPSNTDDV-------VGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHA 65
           +GG+ V  ++ +  + +       +   AR  A D   A  AAKAAFPAW+      R  
Sbjct: 27  IGGEAVPALDGATFETLSPVDLKPLASVARGGAADIDRAAKAAKAAFPAWAAMPGEARKK 86

Query: 66  ILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFA--------GETLRL 117
           +L K AD I AR +E+  +   + G+ L       +R  + F FFA        GETLR 
Sbjct: 87  LLHKIADAIEARAEEIAFVECMDTGQALKFMAKAALRGAENFRFFADRAPEARDGETLRT 146

Query: 118 AGEVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVP 177
            G+V  +         TR P G VGIITPWN P  +  WK+APAL  G T+V KPAE  P
Sbjct: 147 TGQVNMT---------TRVPIGPVGIITPWNTPFMLSTWKIAPALAAGCTVVHKPAEFSP 197

Query: 178 GCSWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASV 237
             +  +V+I   AGLPKGV NLV G G   G+A+ + PD++AI F G + TG  +     
Sbjct: 198 LTARLLVEIAEEAGLPKGVWNLVNGLGEDAGKALTEHPDIRAIGFVGESRTGSMIMKQGA 257

Query: 238 EHNRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFV 297
              ++   E+GGKNP +V  DADL  A +AAV   +   G+RCT+SSR++V   I++ F 
Sbjct: 258 GTLKRVHFELGGKNPVIVFADADLERAADAAVFMIYSLNGERCTSSSRLLVEASIYESFT 317

Query: 298 AAMGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTP 357
           A + ER K +VV   L P T +GP++      +   YI IG+ EGA LA GG  +     
Sbjct: 318 AKVAERAKRIVVGHPLDPKTVVGPLIHPVHEKKVLSYIDIGRSEGATLAVGGGKVDGPGD 377

Query: 358 GFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLK 417
           G Y+ P LFT  TN MRI++EEIFGPV + I   D  EALA+ANDT +GL+  + T+ + 
Sbjct: 378 GCYVGPTLFTNVTNGMRIAQEEIFGPVLSAIPFNDEAEALALANDTQYGLTGYLWTSDVT 437

Query: 418 HATHFKRNAEAGMVMVN------LPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVK 471
            A  F    EAGM+ VN      LPT       PFGG K S  G R+ G ++ +FY   K
Sbjct: 438 RAFRFTDALEAGMIWVNSENVRHLPT-------PFGGVKNSGIG-RDGGDHSFDFYMETK 489


Lambda     K      H
   0.317    0.134    0.391 

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: 599
Number of extensions: 27
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: 477
Length of database: 505
Length adjustment: 34
Effective length of query: 443
Effective length of database: 471
Effective search space:   208653
Effective search space used:   208653
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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