GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Caulobacter crescentus NA1000

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate CCNA_00192 CCNA_00192 long-chain-fatty-acid--CoA ligase

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__Caulo:CCNA_00192
          Length = 539

 Score =  224 bits (570), Expect = 9e-63
 Identities = 152/502 (30%), Positives = 246/502 (49%), Gaps = 14/502 (2%)

Query: 47  RYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRL 106
           RY Y+         A AL R G    D+++ ++ N    LE F+  P  G VL   N RL
Sbjct: 40  RYDYAGLAGRAAQAAHALRRLGIKAGDRVTSLAWNTHRHLELFYAAPGIGAVLHTANPRL 99

Query: 107 SPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKA--EIILLEDPDNPSASETARKEVR 164
             +++ Y INH++S  +  +  +   +  +  Q+      ++L D +             
Sbjct: 100 FDEQIVYTINHAESGVLFFERNFQALVERIAPQLTTVKTFVMLSDAERTVPGAVGA---- 155

Query: 165 MTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQ 224
           ++Y  L++G   D +  P+ +E +   L YTSGTTG PKGV++ HR   L+AMA  L   
Sbjct: 156 ISYETLIEG-EPDVIAWPSFDENAGAFLCYTSGTTGDPKGVLYSHRAVVLHAMAGGLNSA 214

Query: 225 MDLN--SVYLWTLPMFHAASWGFSWATVAVGATNVC-LDKVDYPLIYRLVEKERVTHMCA 281
                  V +    ++HA +WG  ++    GA  V   DK+D   +++L+E E VT    
Sbjct: 215 FGFTPFDVVMPCSSLYHATAWGLPFSAPICGAKLVLPADKMDGASLHQLIEGEGVTFTGG 274

Query: 282 APTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQE-IGGYMCHVYGLTETYGP 340
            PT++    D++ +N+ +  +   +++ G+A   A  +  +   G     ++G+TET   
Sbjct: 275 VPTIWTMYLDWLDKNDRRPDSLKKVVIGGSAVPRAMAETFKRRYGVQTLQIWGMTETCPI 334

Query: 341 HSICEWRREWDSLPLEEQAK-LKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGH 399
             +        +L  E   + +  RQG      E+ V   +G+  PWDG+T G +++RG 
Sbjct: 335 GVVATPTPALAALGEEAMDEAIWTRQGRLQFGIELKVETEDGQAAPWDGETSGALLVRGP 394

Query: 400 NVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEK 459
            V   Y++     A    DG+F +GD A +  +G++ I DR KD+I +GGE +SSI +E 
Sbjct: 395 WVVKRYFRKDADAARE--DGFFDTGDIATLDANGFMRITDRQKDVIKSGGEWISSIDLEN 452

Query: 460 TLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVE 519
             +  PGVK  AV G P  KW E     IE  EG ++T+  V+ +   R+  +  P  V 
Sbjct: 453 VAVGCPGVKIAAVIGVPHPKWEERPLLVIETHEGAEVTKAAVLDYLTPRIVKWWTPDDVV 512

Query: 520 FGPIPMTATGKMQKYVLRNEAK 541
           F  +P+TATGK+ K VLR   K
Sbjct: 513 FATVPLTATGKIDKKVLRQAWK 534


Lambda     K      H
   0.319    0.136    0.411 

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: 700
Number of extensions: 34
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: 549
Length of database: 539
Length adjustment: 35
Effective length of query: 514
Effective length of database: 504
Effective search space:   259056
Effective search space used:   259056
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 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