GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Caulo:CCNA_00192 CCNA_00192
           long-chain-fatty-acid--CoA ligase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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