GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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