Alignments for a candidate for liuB in Saccharomonospora cyanea NA-134

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Saccharomonospora cyanea NA-134

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_005457368.1 SACCYDRAFT_RS15120 biotin carboxylase N-terminal domain-containing protein

Query= BRENDA::Q9I299
         (655 letters)



>NCBI__GCF_000244975.1:WP_005457368.1
          Length = 1833

 Score =  378 bits (970), Expect = e-108
 Identities = 261/664 (39%), Positives = 357/664 (53%), Gaps = 32/664 (4%)

Query: 9   QRLLVANRGEIACRVMRSARALG------IGSVAVHSDIDRHARHVAEADIAVDLGGAKP 62
           +R+ + NRGE A R++ + R         + +VA ++D DR A  V EAD A  LG A  
Sbjct: 3   RRVAIVNRGEAAMRLIHAVRERNAEGGPRLETVAFYTDADRGATFVREADEAYCLGPAS- 61

Query: 63  ADSYLRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSK 122
           A  YL    +  A + + A A+  G+GF++E+  FA  C+  G+ F+GP A A+  +G K
Sbjct: 62  ARPYLDLGVLERALVETKADAVWVGWGFVAEDPAFAELCDRLGVTFVGPSAEAMRRLGDK 121

Query: 123 SAAKALMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAE 182
             AK L EE GVP+ P   G   DL+  R  A RIGYP++LKA AGGGG+G++VV  EAE
Sbjct: 122 IGAKLLAEEVGVPVAPWSRGPVDDLDAARAAAERIGYPLMLKATAGGGGRGIRVVSSEAE 181

Query: 183 LAEALSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQ 242
           LA+A    + EA+ AFG   + +E+ +   RHVE+QV AD  G    L  RDCSIQRR+Q
Sbjct: 182 LADAYERTRMEAERAFGSGVVFLERLVTGARHVEVQVIADGQGTAWALGVRDCSIQRRNQ 241

Query: 243 KVVEEAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFF-FMEMNTRLQV 301
           KV+EE+ +P L  E    +  +A R   A+GY GA TVEFL     + F F+E+NTRLQV
Sbjct: 242 KVIEESASPLLTPEQTGELKASAERLVLAVGYRGAATVEFLYHPGEKLFAFLEVNTRLQV 301

Query: 302 EHPVTEAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRL 361
           EHP+TEA TG+DLV  Q+ VA G    L  E+    GHA+E RL AEDP+ DF PA GR+
Sbjct: 302 EHPITEATTGMDLVKAQLHVAAGG--KLEGERPRELGHAVEARLNAEDPDRDFAPAPGRI 359

Query: 362 MLYREAAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSV-- 419
            L     AGPG RVD+GV EGD +   +D M+AK+IA+G  R+EA  RL   +A+TSV  
Sbjct: 360 SLL-TFPAGPGIRVDTGVSEGDTIPADFDSMIAKIIAYGRDRDEALARLRRAVADTSVLI 418

Query: 420 GGLRTNLAFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWLQSEP 479
            G  TN +FL  +L  P    A  DTG+I R + +          H   A A A + S  
Sbjct: 419 EGGSTNKSFLLDLLDAPEVVEASADTGWIDRVRGE---GRLRATRHAGIALAVAAIDSYT 475

Query: 480 GHRRDDDPHSPWSRNDG---WRSALARESDLMLRCRDERRCVRLR---------HASPSQ 527
                +  H   + + G    R   +R  DL LR    R  V               P+ 
Sbjct: 476 EAEHAEQQHLLSTAHGGRPQVRHVGSRTVDLKLRGTTYRVTVARTGPRWFGVAIEDGPAT 535

Query: 528 YRLDGDDLVSRVDGVTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSA 587
           +R+D +  + R    T +  A  R  +      G +  +E    +     +    G + +
Sbjct: 536 HRVDLE--IERHGEATGQLVAHGRRYRFVTGTHGPVHVVEVDGTV--HRISRDEGGVVRS 591

Query: 588 PMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPL 647
           P    +V   VE G  VEAGA ++VLE+MKME  +RAP   V++    S G  VE G PL
Sbjct: 592 PAPALVVAAPVEVGAEVEAGAPVLVLESMKMETVLRAPFRAVLRERPVSIGSQVEAGAPL 651

Query: 648 VELD 651
           + L+
Sbjct: 652 LRLE 655


Lambda     K      H
   0.319    0.135    0.397 

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: 2522
Number of extensions: 124
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 655
Length of database: 1833
Length adjustment: 46
Effective length of query: 609
Effective length of database: 1787
Effective search space:  1088283
Effective search space used:  1088283
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: 58 (26.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 2024 update 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