Alignments for a candidate for liuD in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuD in Ruegeria conchae TW15

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_010442783.1 G7G_RS0117675 methylcrotonoyl-CoA carboxylase

Query= reanno::Smeli:SM_b21122
         (535 letters)



>NCBI__GCF_000192475.1:WP_010442783.1
          Length = 535

 Score =  837 bits (2161), Expect = 0.0
 Identities = 416/533 (78%), Positives = 460/533 (86%), Gaps = 1/533 (0%)

Query: 4   LRSHISPSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRLATL 63
           L+S   P+SE FKANRAA  +A+A I +A   A  GGGE +R RH SRGK+LPR R+A L
Sbjct: 3   LKSKAIPTSEGFKANRAAHLDALARISEAAEAARMGGGERSRARHESRGKMLPRRRVANL 62

Query: 64  IDPGTPFLEVGATAAYGMYNDDAPGAGLITGIGRISARECMIVCNDPTVKGGTYYPLTVK 123
           +DPG+PFLE+GATAA+GMY   AP AG+I GIGR+  RE M+VCND TVKGGTYYP+TVK
Sbjct: 63  LDPGSPFLEIGATAAHGMYGGAAPCAGVIAGIGRVQGREVMVVCNDATVKGGTYYPMTVK 122

Query: 124 KHLRAQEIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAGIPQIAV 183
           KHLRAQEIA EN LPC+YLVDSGGANLPNQDEVFPDRDHFGRIFYNQA MSA GI QIAV
Sbjct: 123 KHLRAQEIAEENHLPCIYLVDSGGANLPNQDEVFPDRDHFGRIFYNQARMSAKGIAQIAV 182

Query: 184 VMGSCTAGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGADVHTRLSG 243
           VMGSCTAGGAYVPAMSD  IIV++QGTIFLAGPPLV+AATGEVVSAEDLGG DVHTRLSG
Sbjct: 183 VMGSCTAGGAYVPAMSDVTIIVKEQGTIFLAGPPLVKAATGEVVSAEDLGGGDVHTRLSG 242

Query: 244 VADHLARDDAHALALARRAVSALNREKPWTVERIEP-EPPLYDPEEIAGIVPADLKTPYE 302
           VAD+LA DDAHALALARRAV +L         R E  E P YDPEE+ G+VPADL+TPY+
Sbjct: 243 VADYLAEDDAHALALARRAVGSLGGAGLKPGLRFEASEEPDYDPEEVLGVVPADLRTPYD 302

Query: 303 IREVIARLVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAVKGAHFVEL 362
           IREVIARLVDGSRFDEFK RFG TLV GFAHV G PVGI+ANNGVLFSE+A KGAHFVEL
Sbjct: 303 IREVIARLVDGSRFDEFKPRFGETLVTGFAHVKGCPVGIIANNGVLFSEAAQKGAHFVEL 362

Query: 363 CAQRRIPLVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGGSFGAGNY 422
           C+QR+ PLVFLQNITGFMVGRKYE EGIA+HGAK+VTAVAT  VPKITMLVGGSFGAGNY
Sbjct: 363 CSQRKTPLVFLQNITGFMVGRKYENEGIARHGAKMVTAVATTSVPKITMLVGGSFGAGNY 422

Query: 423 GMCGRAFSPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEEARFRQPVL 482
           GM GRA+ PRFLWTWPNSRISVMGGEQAAGVL++V+ + ++R G  WS EEEA F++P L
Sbjct: 423 GMAGRAYQPRFLWTWPNSRISVMGGEQAAGVLATVKRDGIERQGGTWSAEEEAEFKRPTL 482

Query: 483 DLFERQSHPLYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEETRFGLFRM 535
           D+FE QSHPLYASARLWDDG+IDPRKSRDVLALSLSAALNAPIEETRFG+FRM
Sbjct: 483 DMFEEQSHPLYASARLWDDGIIDPRKSRDVLALSLSAALNAPIEETRFGVFRM 535


Lambda     K      H
   0.320    0.136    0.404 

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: 951
Number of extensions: 35
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: 535
Length adjustment: 35
Effective length of query: 500
Effective length of database: 500
Effective search space:   250000
Effective search space used:   250000
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 (21.8 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