Alignments for a candidate for liuD in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuD in Stenotrophomonas chelatiphaga DSM 21508

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_057507595.1 ABB28_RS05085 methylcrotonoyl-CoA carboxylase

Query= BRENDA::Q9I297
         (535 letters)



>NCBI__GCF_001431535.1:WP_057507595.1
          Length = 536

 Score =  774 bits (1999), Expect = 0.0
 Identities = 385/536 (71%), Positives = 442/536 (82%), Gaps = 1/536 (0%)

Query: 1   MAILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARHSARGKLLVRERI 60
           M+ L TQ++  S  F +N + M   V+ L   L R   GG  AA+++H+ARGKLLVRERI
Sbjct: 1   MSTLSTQLHAGSEPFESNRSAMQAVVDDLHATLARTALGGSEAARSKHTARGKLLVRERI 60

Query: 61  NRLLDPGSPFLELSALAAHEVYGEEVAAAGIVAGIGRVEGVECMIVGNDATVKGGTYYPL 120
           + LLD GS FLE++ LAAH +Y + V  AG+VAGIGRV GVEC+IV NDATVKGGTYYP+
Sbjct: 61  DALLDAGSAFLEIAPLAAHGMYEDAVPCAGVVAGIGRVSGVECVIVANDATVKGGTYYPM 120

Query: 121 TVKKHLRAQAIALENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSARGIPQ 180
           TVKKHLRAQ IA +NRLPCIYLVDSGGA LP QDEVFPDR+HFGRIF+NQAN+SA+GIPQ
Sbjct: 121 TVKKHLRAQEIAEQNRLPCIYLVDSGGAFLPLQDEVFPDRDHFGRIFYNQANLSAQGIPQ 180

Query: 181 IAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEELGGADVHCK 240
           IA VMGSCTAGGAYVPAMSDETV+VREQ TIFL GPPLVKAATGEVVSAE+LGGADVH +
Sbjct: 181 IACVMGSCTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAATGEVVSAEDLGGADVHTR 240

Query: 241 VSGVADHYAEDDDHALAIARRCVANLNWRK-QGQLQCRAPRAPLYPAEELYGVIPADSKQ 299
           +SGVADH A++D  ALA  R  +A LNW K +  +  + P+ PL+P ++LYGVIPAD+++
Sbjct: 241 LSGVADHMADNDLQALARVRAIIAQLNWCKPEPAMALQPPQEPLFPPQDLYGVIPADTRK 300

Query: 300 PYDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHF 359
           P+DVREVIARLVDGS FDEFK  +G+TLV GFAHLHGYP+ I+ANNGILF+E+A KGAHF
Sbjct: 301 PFDVREVIARLVDGSRFDEFKPRYGSTLVTGFAHLHGYPVGIIANNGILFSESALKGAHF 360

Query: 360 IELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFTVLIGGSFGA 419
           IEL  QR IPL+FLQNITGFMVG+KYE GGIAK GAKLV AVACA+VPKFTV+IGGSFGA
Sbjct: 361 IELCTQRNIPLVFLQNITGFMVGRKYEQGGIAKDGAKLVMAVACAKVPKFTVVIGGSFGA 420

Query: 420 GNYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAKIKA 479
           GNYGMCGRAY P FLWMWPNARIGVMGGEQAA VLA VKR+  E  G      EE   KA
Sbjct: 421 GNYGMCGRAYSPNFLWMWPNARIGVMGGEQAASVLATVKRDGIEAKGGAWAAAEEEAFKA 480

Query: 480 PILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNAPIEPTAFGVFRM 535
           PI +Q+EHQGHPYY+SARLWDDG+IDPA TR VLALALSA+LNAP   T FGVFRM
Sbjct: 481 PIRDQFEHQGHPYYASARLWDDGIIDPADTRRVLALALSASLNAPARETRFGVFRM 536


Lambda     K      H
   0.321    0.137    0.409 

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: 976
Number of extensions: 36
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: 535
Length of database: 536
Length adjustment: 35
Effective length of query: 500
Effective length of database: 501
Effective search space:   250500
Effective search space used:   250500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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