GapMind for catabolism of small carbon sources

 

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

Align Probable enoyl-CoA hydratase echA12; EC 4.2.1.17 (uncharacterized)
to candidate WP_011384970.1 AMB_RS13030 enoyl-CoA hydratase

Query= curated2:Q7U004
         (285 letters)



>NCBI__GCF_000009985.1:WP_011384970.1
          Length = 272

 Score =  140 bits (354), Expect = 2e-38
 Identities = 91/264 (34%), Positives = 138/264 (52%), Gaps = 25/264 (9%)

Query: 28  EIAQITLNRPERMNSMAFDVMVPLKEALAQVSYDNSVRVVVLTGAGRGFSSGADHKSAGV 87
           ++A +TLNRP+R N + FD    L++    + Y + V+ V++TG+G  F SG D      
Sbjct: 21  KVATLTLNRPDRKNPLTFDSYGELRDLFENMVYADDVKAVIVTGSGGNFCSGGD------ 74

Query: 88  VPHVENLTRPTYALRSMELLD------DVILMLRRLHQPVIAAVNGPAIGGGLCLALAAD 141
              V  +  P   +   ELL+      D +  +R   QP+IAA++G   G G  L  A+D
Sbjct: 75  ---VHEIIGPLTKMDMPELLEFTRMTGDAVRAMRNAPQPIIAAIDGICAGAGTMLGCASD 131

Query: 142 IRVASSSAYFRAAGINNGLTASELGLSYLLPRAIGSSRAFEIMLTGRDVSAEEAERIGLV 201
           IR+ ++ +      +  GL  +++G   LLPR IG SRA E++ TGR +  EEAER+G  
Sbjct: 132 IRLGTARSKVAFLFVRVGLAGADMGACTLLPRLIGLSRAAELLYTGRAMGGEEAERVGYY 191

Query: 202 SRQVPDEQLLDACYAIAARMAGFSRPGIELTKRTLWS----GLDAASLEAHMQAEGLGQL 257
           +     E+LLDA   +A  +A     G  +TK+ LW     GL    +EA  QA+     
Sbjct: 192 NSLHAPEELLDAANKLAQSLANGPTFGHAMTKKMLWQEWNHGL-GECIEAEAQAQA---- 246

Query: 258 FVRLLTANFEEAVAARAEQRAPVF 281
            + + T +FE A  A A ++APVF
Sbjct: 247 -ICMQTKDFERAYVAFANKQAPVF 269


Lambda     K      H
   0.320    0.133    0.376 

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: 162
Number of extensions: 8
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: 285
Length of database: 272
Length adjustment: 25
Effective length of query: 260
Effective length of database: 247
Effective search space:    64220
Effective search space used:    64220
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: 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