Aligments for a candidate for acs in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Paraburkholderia bryophila 376MFSha3.1

Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate H281DRAFT_05558 H281DRAFT_05558 fatty-acyl-CoA synthase

Query= metacyc::MONOMER-20124
         (573 letters)



>FitnessBrowser__Burk376:H281DRAFT_05558
          Length = 550

 Score =  501 bits (1291), Expect = e-146
 Identities = 257/544 (47%), Positives = 348/544 (63%), Gaps = 11/544 (2%)

Query: 23  TTSWKSMEGLVQCSANHVPLSPITFLERSSKAYRDNTSLVYGSVRYTWAQTHHRCLKLAS 82
           T+ W    GL   +AN   L+P+TFL+R+ K + D T++VYGS R TW +    C + AS
Sbjct: 3   TSRWND-PGLRPRAANFDALTPVTFLQRAEKVFPDRTAVVYGSHRETWREHAATCRRFAS 61

Query: 83  ALTTHLGISPGDVVATFSYNLPEIYELHFAVPMAGGILCTLNARNDSAMVSTLLAHSEAK 142
           AL    GI  GDVVA    N P +   HFAVPMAG +L T+N R D+  VS +L HSEA+
Sbjct: 62  ALA-RAGIEYGDVVALLMTNTPPMLAAHFAVPMAGAVLNTINTRLDAENVSYILGHSEAR 120

Query: 143 LIFVEPQLLETARAALDLLAQKDIKPPTLVLLTDSESF--TSSSYDHYNHLLANGSDDFE 200
           LI V+ + LE AR A+  L      PP LV   D ++    SS  + Y   LA+G ++  
Sbjct: 121 LIIVDAEFLELARTAVARLQH----PPRLVCFADEQAAFAASSDVEDYVSFLASGDENAS 176

Query: 201 IRRPKNEWDPISINYTSGTTARPKAVVYSHRGAYLNSIATVLLHGMGTTSVYLWSVPMFH 260
             + + EW PI++NYTSGTT RPK VVYSHRGAYL+++++++  G+   + YLW++P+FH
Sbjct: 177 FCKVEEEWTPIAVNYTSGTTGRPKGVVYSHRGAYLSAVSSIISWGVPKAASYLWTLPLFH 236

Query: 261 CNGWCFPWGAAAQGATNICIRKVSPKAIFDNIHLHKVTHFGAAPTVLNMIVNSPEGNLHT 320
           CNGWC PW  A QG  ++C+R+V    I   I+  +VTH+  AP +++ ++         
Sbjct: 237 CNGWCMPWVLALQGGKSVCLRRVDGDKIVQLINDERVTHYCGAP-IVHALIRDRAQQQDL 295

Query: 321 PLPHKVEVMTGGSPPPPKVIARMEEMGFQVNHIYGLTETCGPAANCVCKPEWDALQPEER 380
                V  + GG+PPP  +IA M+ +G Q+ HIYGLTET GPAA C  +P W  L   ER
Sbjct: 296 VFNPAVSALIGGAPPPASLIAAMDAIGVQLTHIYGLTETYGPAAICEQQPAWAELGEAER 355

Query: 381 YALKARQGLNHLAMEEMDVRDPVTMESVRADGATIGEVMFRGNTVMSGYFKDLKATEEAF 440
              KARQG+N+     M V +  + + V ADGA +GE++FRGN  M GY KD ++T+ AF
Sbjct: 356 ADRKARQGVNYALQAGMTVMNCNSSDEVSADGAMMGEIVFRGNMTMMGYLKDSESTDRAF 415

Query: 441 EGGWFRSGDLGVKHEDGYIQLKDRKKDVVISGGENISTVEVETVLYSHEAVLEAAVVARP 500
           +GGWFRSGDL V   DGY+++KDR KD++ISGGENIS+VEVE VLY HE V  AAVVA P
Sbjct: 416 DGGWFRSGDLAVLEPDGYVRIKDRSKDIIISGGENISSVEVEDVLYRHETVAAAAVVAMP 475

Query: 501 DKLWGETPCAFVTLKEGFDNDVSADQIIKFCRDRLPHYMAPKTVVFEELPKTSTGKIQKY 560
           D+ WGE P A V L+EG  +  S D +I  CR++L H+  PK V+F  +PKT+TGKIQK 
Sbjct: 476 DEKWGEVPVAIVELREG--SHASEDALIAHCREQLAHFKCPKRVIFHPIPKTATGKIQKN 533

Query: 561 ILKE 564
           +L+E
Sbjct: 534 VLRE 537


Lambda     K      H
   0.318    0.133    0.408 

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: 822
Number of extensions: 38
Number of successful extensions: 5
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: 573
Length of database: 550
Length adjustment: 36
Effective length of query: 537
Effective length of database: 514
Effective search space:   276018
Effective search space used:   276018
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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, or view the source code.

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