Alignments for a candidate for liuD in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuD in Cereibacter sphaeroides ATCC 17029

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_002719660.1 RSPH17029_RS05945 methylcrotonoyl-CoA carboxylase

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



>NCBI__GCF_000015985.1:WP_002719660.1
          Length = 534

 Score =  832 bits (2149), Expect = 0.0
 Identities = 409/532 (76%), Positives = 462/532 (86%)

Query: 4   LRSHISPSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRLATL 63
           L S + PSSE F+ANRA     IA   +A   AAAGGG  A+ RH +RGKL PR+R+A L
Sbjct: 3   LSSRVLPSSETFRANRAHHLALIAETAEAAAWAAAGGGPAAQARHAARGKLPPRERVAGL 62

Query: 64  IDPGTPFLEVGATAAYGMYNDDAPGAGLITGIGRISARECMIVCNDPTVKGGTYYPLTVK 123
           +DPG+PFLE+GA AA+G+Y+  AP AG+I GIGR+  +E M+VCND TVKGGTYYP+TVK
Sbjct: 63  LDPGSPFLEIGAFAAHGLYDGAAPAAGVIAGIGRVHGQEVMVVCNDATVKGGTYYPMTVK 122

Query: 124 KHLRAQEIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAGIPQIAV 183
           KHLRAQEIAAE RLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQA MSAAGIPQIAV
Sbjct: 123 KHLRAQEIAAECRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQAQMSAAGIPQIAV 182

Query: 184 VMGSCTAGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGADVHTRLSG 243
           VMGSCTAGGAYVPAMSD  IIV  QGTIFLAGPPLV+AATGEVVSAEDLGG +VHTRLSG
Sbjct: 183 VMGSCTAGGAYVPAMSDVTIIVRNQGTIFLAGPPLVKAATGEVVSAEDLGGGEVHTRLSG 242

Query: 244 VADHLARDDAHALALARRAVSALNREKPWTVERIEPEPPLYDPEEIAGIVPADLKTPYEI 303
           VAD+LA DDAHALALARRA+  LNR +P TV    PE P +DPEEI G+VPADL+TP++I
Sbjct: 243 VADYLAEDDAHALALARRALGQLNRTRPETVAWAAPEDPAHDPEEILGLVPADLRTPWDI 302

Query: 304 REVIARLVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAVKGAHFVELC 363
           RE+IARLVDGSRFDEFK RFG TLV GFAH+ G PVGIVANNGVLFSE+A+KGAHFVELC
Sbjct: 303 RELIARLVDGSRFDEFKPRFGETLVTGFAHLMGCPVGIVANNGVLFSEAAIKGAHFVELC 362

Query: 364 AQRRIPLVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGGSFGAGNYG 423
           +QR IPL+FLQNITGFMVGR+YE EGIA+HGAK+VTAVAT  VPKIT+LVGGSFGAGNYG
Sbjct: 363 SQRSIPLIFLQNITGFMVGRRYENEGIARHGAKMVTAVATTAVPKITLLVGGSFGAGNYG 422

Query: 424 MCGRAFSPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEEARFRQPVLD 483
           M GRA+SPRFLWTWPNSRISVMGGEQAAGVL++VR +A++R G  WS EEEA F++P ++
Sbjct: 423 MAGRAYSPRFLWTWPNSRISVMGGEQAAGVLATVRRDAIERQGGHWSAEEEAAFKRPTIE 482

Query: 484 LFERQSHPLYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEETRFGLFRM 535
           +FERQSHPL+ASARLWDDG++DPRKSR+ L LSLSAALNAPI  TRFGLFRM
Sbjct: 483 MFERQSHPLHASARLWDDGIVDPRKSRETLFLSLSAALNAPIAPTRFGLFRM 534


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: 917
Number of extensions: 36
Number of successful extensions: 1
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: 534
Length adjustment: 35
Effective length of query: 500
Effective length of database: 499
Effective search space:   249500
Effective search space used:   249500
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 Apr 10 2024. The underlying query database was built on Sep 17 2021.

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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