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_011384978.1 AMB_RS13070 enoyl-CoA hydratase

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



>NCBI__GCF_000009985.1:WP_011384978.1
          Length = 256

 Score =  209 bits (531), Expect = 6e-59
 Identities = 116/254 (45%), Positives = 160/254 (62%)

Query: 4   ETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAA 63
           E LL    + V L+ +NRP A NALNG++   L + +  L ADP +  IV+TG+ +AFAA
Sbjct: 3   EVLLEKPFDSVVLLRINRPDAKNALNGEVRRLLAEHMTTLGADPSVRAIVMTGNQEAFAA 62

Query: 64  GADIKEMAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAAD 123
           GADIK+MAE+   ++   +       IA   KP+IAAV GYA GGGCEL +  D+I A +
Sbjct: 63  GADIKDMAEVGAIELMQRNNHLLWRAIANCPKPVIAAVNGYAWGGGCELVMHADIIVAGE 122

Query: 124 NARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPAE 183
           NA F QPEV +G++PG GGTQRLTRAVGK KAM M +TG+ +   EA + GL + V P  
Sbjct: 123 NASFSQPEVKVGIMPGAGGTQRLTRAVGKFKAMLMVMTGQAISGVEAGQMGLASVVVPDA 182

Query: 184 SLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQKEGM 243
            ++++ L+ A+ I+     A   IKE +    + +L   +  ER+ F  +FA+ADQKEGM
Sbjct: 183 EVVDKALEIAKTISRMPPVAIAQIKEVLLAGQDASLDTALMLERKAFQLLFASADQKEGM 242

Query: 244 AAFSEKRKPEFTNR 257
            AF EKRKP +  +
Sbjct: 243 KAFIEKRKPTYQGK 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: 161
Number of extensions: 4
Number of successful extensions: 2
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: 256
Length adjustment: 24
Effective length of query: 233
Effective length of database: 232
Effective search space:    54056
Effective search space used:    54056
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