Aligments for a candidate for hcl in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19285 HSERO_RS19285 long-chain
           fatty acid--CoA ligase
          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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources