GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sphingomonas histidinilytica UM2

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_079648207.1 B5X82_RS11035 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_900167915.1:WP_079648207.1
          Length = 528

 Score =  372 bits (954), Expect = e-107
 Identities = 211/520 (40%), Positives = 303/520 (58%), Gaps = 11/520 (2%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           FN+ RDV      + R    A++W +  +G   + S+ E+++ ++R  + L + G+ +GD
Sbjct: 11  FNFTRDVMGR-WAELRPDDPAMVWTE-PSGTVIERSFAEMAIAASRAAAVLAEAGVGRGD 68

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157
            V ++       W + L  I  G +  P  T L   ++ YR        +++    A  +
Sbjct: 69  TVLILLNREIEWWELMLGCIAIGAIASPGTTQLMAKDIAYRHRAAAARCVVASGEMAERV 128

Query: 158 EEALGSLKVEKFLIDGKRETWNSLEDESSNAEP----EDTRGEDVIINYFTSGTTGMPKR 213
           + AL    + +  + G R  W    +  + A P     DT  ++  + YFTSGTTG PK 
Sbjct: 129 DTALAGEDIARLHVGGPRSGWIDYGERRAAATPIATAADTGFDEDALCYFTSGTTGQPKM 188

Query: 214 VIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEG 273
            IHT        IT +  + ++  DLH NLS TGWAK AWSS F+P L+GAT+  +++  
Sbjct: 189 TIHTHGYMLAHRITGSYWLDLKPGDLHWNLSDTGWAKAAWSSLFAPWLMGATIF-VHHSP 247

Query: 274 KLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKIW 333
             D    L  +E + VT+ CAPPTA+R F+  DL   RF+ LR  VSAGEPLNPEVI +W
Sbjct: 248 GFDPVATLDLLERMPVTTLCAPPTAYRMFVRSDLTGRRFDTLRHCVSAGEPLNPEVIDLW 307

Query: 334 KDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVG 393
           K      I D YGQTET  +  N      + GSMG+P P +D+ ++D EG  +    E G
Sbjct: 308 KAATGRDIHDGYGQTETVLLCAN-RVGAARQGSMGRPAPDFDLAVIDGEGNRLPADVE-G 365

Query: 394 HITVKL-NPRPIGLFLGYSDE-KKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKT 451
            + +++    P GLF  Y D+ ++  ++ R+G+Y TGD+A  D +GYF+FVGR DDVI +
Sbjct: 366 DVALRIAEGHPPGLFARYRDDPQRTADTKRDGWYLTGDRAIVDADGYFWFVGRSDDVILS 425

Query: 452 SDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREK 511
           S YR+GPFEVESAL EHPAVAE+AVV  PD  R ++VKA++VL  G+ PS+ L   +++ 
Sbjct: 426 SGYRIGPFEVESALFEHPAVAESAVVSSPDPTRGEVVKAFVVLAAGFEPSEALVGMLQDH 485

Query: 512 MKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEK 551
           +K+  +PYK PR IEFV  LPKT+SGKIRR ELR RE E+
Sbjct: 486 VKSTTAPYKYPRKIEFVTSLPKTVSGKIRRKELRDREWER 525


Lambda     K      H
   0.318    0.137    0.402 

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: 714
Number of extensions: 37
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: 564
Length of database: 528
Length adjustment: 35
Effective length of query: 529
Effective length of database: 493
Effective search space:   260797
Effective search space used:   260797
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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