Alignments for a candidate for liuB in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Halomonas desiderata SP1

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate WP_086510401.1 BZY95_RS13285 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::pseudo1_N1B4:Pf1N1B4_3984
         (651 letters)



>NCBI__GCF_002151265.1:WP_086510401.1
          Length = 681

 Score =  636 bits (1641), Expect = 0.0
 Identities = 360/678 (53%), Positives = 449/678 (66%), Gaps = 44/678 (6%)

Query: 8   TLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQI 67
           TLLVANRGEIACRVMRTA+A+GL TVAV+S  D +ARH READ  V LG + A +SYL++
Sbjct: 13  TLLVANRGEIACRVMRTARAMGLRTVAVYSDADANARHVREADEAVRLGPAAARESYLKV 72

Query: 68  DKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALM 127
           + ++ AAK +GA AIHPGYGFLSEN  F +A++AAG+ F+GPPASAI AMG KSAAKA M
Sbjct: 73  EAVVEAAKRTGAGAIHPGYGFLSENGAFVQALDAAGITFVGPPASAIAAMGDKSAAKARM 132

Query: 128 ETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187
             AGVPLVPGYHG+ QD    +   ++IGYPVLLKA+AGGGGKGM+VVE   Q   AL  
Sbjct: 133 ANAGVPLVPGYHGDDQDDALLKSEADKIGYPVLLKASAGGGGKGMRVVEAPEQFQAALDG 192

Query: 188 AQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247
            +RE+ ++FGD+RML+EKYL +PRHVE+QVF D HGN +YL ERDCS+QRRHQKV+EEAP
Sbjct: 193 CRRESQAAFGDTRMLIEKYLTQPRHVEVQVFCDSHGNGVYLFERDCSVQRRHQKVLEEAP 252

Query: 248 APGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAI 307
           APG++ ELRR MGEAAVR+A+ IGYVGAGTVEFLLD  G F+FMEMNTRLQVEHPVTE I
Sbjct: 253 APGMTAELRREMGEAAVRAAKEIGYVGAGTVEFLLDKDGSFYFMEMNTRLQVEHPVTEMI 312

Query: 308 TGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRESAA 367
           TG DLV WQ+RVA GE LP+ Q+++ + GH+ E RLYAEDP  DFLPATGRL  +     
Sbjct: 313 TGQDLVEWQLRVAMGETLPLQQEELTITGHSFEARLYAEDPEQDFLPATGRLERFAMDLK 372

Query: 368 GPGR-----RVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKT 422
           G G      R+DSGVE GD +S  YDPML KLI  G+DR+QA   L   L    + G+ T
Sbjct: 373 GAGLDPRQVRLDSGVETGDVVSMHYDPMLAKLIVHGDDRDQALSTLNRALAALDVQGVVT 432

Query: 423 NINFLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRA 482
           N  FL+R+  HPAF  AELDT FI +  E  L AP   S E +  AA       +   R 
Sbjct: 433 NRAFLQRLATHPAFRNAELDTRFIEK-NEATLFAPKQYSIEEYAGAALI---GLNQLARE 488

Query: 483 DDLSSPWGIGNGFRAGLPTEITLHLSCE---------------EQDRA-------LTLG- 519
            +  SPW   +GFR   P  I + L C+               E  RA       LT+G 
Sbjct: 489 CESDSPWDRHDGFRLNAPHTIRISL-CDPSIAQVHDAEGVVVVEGTRASGADPWDLTIGG 547

Query: 520 -DADAHTAQLKGEYLLTEHNGLRRQHRAIRRGDTLYL-QWDGEL----RRIESYDPISAV 573
               A    L+G+ +    NG RR+ +A R G+ + +    GE     RRI++ D     
Sbjct: 548 ETLTARLQHLEGDAVAVTLNGHRRRLQARRDGNVVVMVDPRGETRLFWRRIDAID----- 602

Query: 574 EASHSHQGGLTAPMNGSIVRVLVEAGQTVEAGAQLVVLEAMKMEHSIRAPHAGIIKALYC 633
              H  +  LTAPM+G++V +LVEAGQ VE G  L+V+EAMKMEH++ AP  G +++ + 
Sbjct: 603 HGHHEAESTLTAPMHGTVVALLVEAGQKVEKGMPLMVMEAMKMEHTMTAPADGHVESFHF 662

Query: 634 QEGEMVSEGSALVELEHA 651
             G+ V +G  L+E   A
Sbjct: 663 NAGDTVGQGDVLLEFAPA 680


Lambda     K      H
   0.318    0.134    0.386 

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: 1184
Number of extensions: 56
Number of successful extensions: 6
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: 651
Length of database: 681
Length adjustment: 38
Effective length of query: 613
Effective length of database: 643
Effective search space:   394159
Effective search space used:   394159
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: 54 (25.4 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