GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Novosphingobium barchaimii LL02

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_059151871.1 V474_RS12920 enoyl-CoA hydratase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>NCBI__GCF_001046635.1:WP_059151871.1
          Length = 255

 Score =  129 bits (323), Expect = 8e-35
 Identities = 88/247 (35%), Positives = 132/247 (53%), Gaps = 13/247 (5%)

Query: 18  VLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGA-DNFFCAGGNLNRLLENR 76
           V+TL+ P  RNAL  ++      A    E D ++R  ++TG+ D  FCAGG+L  ++E  
Sbjct: 16  VITLNRPEQRNALTAEVREGLRAAWARFEADDALRIAILTGSGDKAFCAGGDLKEMVETG 75

Query: 77  AKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVM 136
              P       D+ A     + LS KP IAAV+G A   G+ +A ACDL VA+  AKF +
Sbjct: 76  MAVPPR-----DMYALPYDTIELS-KPTIAAVNGVAFAGGWMIAQACDLCVASTAAKFAI 129

Query: 137 SYARVGLTPDGGGSWF--LAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARD 194
           +  +VG     G  W   L   + +++  E+++ GKPI AAR +E+G+VN+L +PG   D
Sbjct: 130 TEVKVGR----GSPWAAPLIHMIGQRIFMEIVLTGKPIDAARAYEIGLVNRLAQPGAVLD 185

Query: 195 AAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFL 254
           AA+  A E+ + +P SV   +  V  +     S  L A R     + + ++  EG  AF 
Sbjct: 186 AAIELAREVLEGAPLSVKAARETVMLSTEMGRSAALAAARSAHEHTYNSQDAQEGPRAFA 245

Query: 255 EKRAPVY 261
           EKR PV+
Sbjct: 246 EKRRPVW 252


Lambda     K      H
   0.317    0.132    0.377 

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: 153
Number of extensions: 11
Number of successful extensions: 4
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: 262
Length of database: 255
Length adjustment: 24
Effective length of query: 238
Effective length of database: 231
Effective search space:    54978
Effective search space used:    54978
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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