Alignments for a candidate for liuB in Halioglobus japonicus S1-36

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Halioglobus japonicus S1-36

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_084200258.1 C0029_RS03860 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::SB2B:6937189
         (673 letters)



>NCBI__GCF_002869505.1:WP_084200258.1
          Length = 658

 Score =  571 bits (1471), Expect = e-167
 Identities = 315/666 (47%), Positives = 437/666 (65%), Gaps = 28/666 (4%)

Query: 4   KLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSYLRG 63
           KLLIANRGEIA RVIRTARDMG +TVAVYS+AD +A HV+ AD++  +G +A   SYL  
Sbjct: 6   KLLIANRGEIAVRVIRTARDMGYRTVAVYSEADANALHVSEADQAVCIGPAAVNESYLVA 65

Query: 64  ELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAKLIM 123
           + I+  A+  GA+AIHPGYGFLSENA F+RACE +GI F+GP  DAI+ MGSK  +K+ M
Sbjct: 66  DNILKAARLTGADAIHPGYGFLSENADFSRACEDAGIVFIGPRPDAIELMGSKRLSKIAM 125

Query: 124 EKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAAIDS 183
            +AGVP +PGY   DQSD TLLA+A  IG+PL++KA+ GGGG+GMR+V    EL   I +
Sbjct: 126 IEAGVPCIPGYQDADQSDDTLLAKAADIGFPLMVKASAGGGGRGMRLVFEARELAEQIRT 185

Query: 184 ARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVEEAP 243
           AR EA S+FG+ +L++ER + +PRHVE+QVFAD  GN VYL +RDCSIQRRHQKVVEEAP
Sbjct: 186 ARSEAESAFGSGELILERAVLEPRHVEIQVFADEHGNAVYLGERDCSIQRRHQKVVEEAP 245

Query: 244 APGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVTEMV 303
           +P +   LR++MGEAAV AAKA +YRGAGTVEFL+D D +F+F+EMNTRLQVEHPVTE++
Sbjct: 246 SPFVDPQLRQRMGEAAVNAAKACNYRGAGTVEFLVDKDKNFYFLEMNTRLQVEHPVTELI 305

Query: 304 TGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLREPEP 363
           TGQDLV WQL VA+G QLPL Q E+ + GHA EVR+YAEDP N F+P +G +     PE 
Sbjct: 306 TGQDLVAWQLKVASGEQLPLTQDEVSLSGHAVEVRLYAEDPRNNFMPQTGTVRLWEYPER 365

Query: 364 SRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNIEFL 423
           +  +R+D G+++   +S +YDPMIAK+I +   R  A+ RL  A+ D ++ G+ +N  FL
Sbjct: 366 A-GLRMDHGIQQGQEVSPFYDPMIAKVIAYGSDRAEAIRRLASAVQDTQLLGMNNNKLFL 424

Query: 424 SNIAEHPAFAQANFSTDFIGRY--GDALIGDSRDEADTAFVLAVLTQLRLREA-VSQDVA 480
            N+  H  FAQ   +T FI ++   D  +   +    T    A+L Q +   A    D +
Sbjct: 425 QNVLRHEVFAQGEATTAFIEQHFSADISMDQKKPRQATLARAALLFQAQATAAGPGSDAS 484

Query: 481 GHDPFSPWSSLKGFRLSSPRRHSVTLLDDAHQSRSAELTESNGRYQLCLNDKLIELS-GS 539
            H+P +  ++ +              L    Q+++  +TE NG Y++ + ++   L+  +
Sbjct: 485 WHNPAAAATTYQ--------------LAFDGQAQAIAITEGNGSYEVAVGEERHSLTLVA 530

Query: 540 IEDSELKCEINGHKMKVTVSLEDGGLTVFLSSGSYHFREVLGQVLEETASS-----EDKL 594
           + DSE  C    + ++ ++     G T++L  G+ HF  ++  V  + A++       +L
Sbjct: 531 LSDSE--CVYIDNGVRESMRFAFAGNTLYLDDGTGHF--IIENVTYQPAAAAGGAGSGQL 586

Query: 595 KAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGELVSDGT 654
           KA M+G +V  LV  GD V AGQ L+V+EAMKME+ ++A   G+V+      G+ V    
Sbjct: 587 KASMDGAIVDVLVTEGDTVEAGQTLVVLEAMKMEHALKAGISGIVTAISCETGQQVKSKQ 646

Query: 655 LLLALE 660
           LL  +E
Sbjct: 647 LLATIE 652


Lambda     K      H
   0.317    0.134    0.380 

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: 1110
Number of extensions: 44
Number of successful extensions: 4
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: 673
Length of database: 658
Length adjustment: 38
Effective length of query: 635
Effective length of database: 620
Effective search space:   393700
Effective search space used:   393700
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.

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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