GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Herbaspirillum seropedicae SmR1

Align 4-hydroxybenzoate-CoA ligase (EC 6.2.1.27); 3-hydroxybenzoate-CoA ligase (EC 6.2.1.37) (characterized)
to candidate HSERO_RS19285 HSERO_RS19285 long-chain fatty acid--CoA ligase

Query= BRENDA::Q5P0J2
         (493 letters)



>FitnessBrowser__HerbieS:HSERO_RS19285
          Length = 566

 Score =  133 bits (335), Expect = 1e-35
 Identities = 149/519 (28%), Positives = 215/519 (41%), Gaps = 57/519 (10%)

Query: 17  AIECDDEKVSYAVLRDRVSRAAGAW-KTLGLQPGNRVIVFAPDSVDWVVAYLGAIWAGGV 75
           A  C  + +SY  L D +SRA G W + LGLQ G RV +  P+ + + +A    + AG  
Sbjct: 41  AYVCMGKYLSYREL-DSLSRALGGWLQGLGLQKGARVAIMMPNVLQYPIAIAAILRAGYT 99

Query: 76  AIGVNPRLSMNEFAPILNE-------------CEPRFVWCETEQARALVAE--------- 113
            + VNP  +  E    L +             C  + V   T     +VA          
Sbjct: 100 VVNVNPLYTARELEHQLKDSGAEAIFVLENFACTLQKVVAHTNIKHIVVASMGELLGALK 159

Query: 114 -------ARTVAEIVA----DGPGTSNWATHLAAAEAVAPLERATEDAALWIGTSGTTGV 162
                   R V ++V         T + A   A  + + P+    +D A    T GTTGV
Sbjct: 160 GTLVNLVVRHVKKLVPAWSLPNAITFSQALSQARGKTLQPVTLTHDDIAFLQYTGGTTGV 219

Query: 163 PKGVVHAQRT----VTNAHSFACGILGL-TAADRLY--ASSKLFFAYALGNSLFAGLRVG 215
            KG V   R     V  A  +    L      D+L    +  L+  +AL      G R G
Sbjct: 220 AKGAVLTHRNLVANVLQAEEWLTPALKAGKPIDQLVFVCALPLYHIFALTVCNMLGTREG 279

Query: 216 ATVILDRQWPTAERVEYMVEKYRPTLLFSVPTLYRKMLQTGVARRIAQYGIRHCVSAGEA 275
           A  +L             + KY+     +V TLY  +L      R+   G R CV  G A
Sbjct: 280 ALNLLIPNPRDIPGFVKELAKYKVNTFPAVNTLYNALLNNADFARLDFSGYRCCVGGGMA 339

Query: 276 LPLAVRQDWREATGHTLISGYGTSETLCLMLFS----DDDSGLM-RPTPLTEVRHADDVD 330
           +  +V   W++ TG  +I GYG SET  +   +    D+ +G +  P P TE    DD  
Sbjct: 340 VQKSVADKWKKLTGCPIIEGYGLSETSPIASANPCTIDEYTGTIGLPLPSTEFAILDDDG 399

Query: 331 PDV----PQRVWIRHSAVALGYWERPEAQADGFR-DGWFSPGDMFLRHADGRLEYTGRND 385
             V    P  + IR   V  GYW+RP+  A     DG+F  GD+ +    G  +   R  
Sbjct: 400 QPVPLGQPGEIAIRGPQVMPGYWQRPDETAKVMTPDGFFKTGDIGVMDERGYTKIVDRKK 459

Query: 386 DMLKIAGQWVSTLWVEQSLASVCGETLHQIASVGVSSADGLTALAV-LAVASPERRSEAR 444
           DM+ ++G  V    VE  +A   G  + + A VGV   D  T  AV L V   ++   A 
Sbjct: 460 DMILVSGFNVYPNEVEGVVAQHPG--VLECACVGV--PDEHTGEAVKLFVVRKDKTLSAA 515

Query: 445 QRMDEGIATLPGHRRPRWVHWLDELPLTPTGKLQRGRLR 483
           Q MD       G+++P+++ + DELP T  GK+ R  LR
Sbjct: 516 QLMDYCKEQFTGYKKPKYIEFRDELPKTNVGKILRRELR 554


Lambda     K      H
   0.320    0.133    0.414 

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: 594
Number of extensions: 30
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 493
Length of database: 566
Length adjustment: 35
Effective length of query: 458
Effective length of database: 531
Effective search space:   243198
Effective search space used:   243198
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 (21.8 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