GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Magnetospirillum magneticum AMB-1

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_011383294.1 AMB_RS04340 enoyl-CoA hydratase

Query= reanno::psRCH2:GFF2389
         (257 letters)



>NCBI__GCF_000009985.1:WP_011383294.1
          Length = 261

 Score =  145 bits (367), Expect = 6e-40
 Identities = 98/254 (38%), Positives = 136/254 (53%), Gaps = 7/254 (2%)

Query: 4   ETLLVDIQER-VALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFA 62
           ET+L+   E  VA +TLNRP+A NAL+  L+SEL+  L ++  DP +  +VL  +  AF 
Sbjct: 5   ETILLRRDEAGVATLTLNRPEARNALSVALMSELDSELARIARDPAVRVVVLAANGPAFC 64

Query: 63  AGADIKEMAELTYPQIYLDDFFADADRIATR----RKPLIAAVAGYALGGGCELALLCDM 118
           AG D+KEM  L   +  +   FA   R+ T      +P+IA V   A   GC+L   CD+
Sbjct: 65  AGHDLKEMRALQ-GRDEVAAVFALCSRVMTAIVRLPQPVIAKVHAMATAAGCQLVASCDL 123

Query: 119 IFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVAR 178
            +AA  A+F  P VN+G+         L+R VG+ +AM+M L+GR ++A  AER GLV  
Sbjct: 124 AYAATEAKFATPGVNIGLFCSTPMVA-LSRGVGRKQAMEMLLSGRPINAGTAERWGLVNH 182

Query: 179 VFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATAD 238
           V  AE+L  E    AR+IA KS     + KE+  R  E  L +      +V        D
Sbjct: 183 VVAAEALDSEVASMARLIASKSAHTLKVGKEAFYRQLEMGLDDAYALASKVMTENMLAMD 242

Query: 239 QKEGMAAFSEKRKP 252
             EG+ AF EKR P
Sbjct: 243 AAEGIDAFLEKRPP 256


Lambda     K      H
   0.321    0.135    0.375 

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: 145
Number of extensions: 7
Number of successful extensions: 3
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: 257
Length of database: 261
Length adjustment: 24
Effective length of query: 233
Effective length of database: 237
Effective search space:    55221
Effective search space used:    55221
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 (21.9 bits)
S2: 47 (22.7 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