GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Shewanella halifaxensis HAW-EB4

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_012277951.1 SHAL_RS14880 enoyl-CoA hydratase

Query= CharProtDB::CH_091794
         (261 letters)



>NCBI__GCF_000019185.1:WP_012277951.1
          Length = 269

 Score =  164 bits (415), Expect = 2e-45
 Identities = 87/243 (35%), Positives = 133/243 (54%), Gaps = 1/243 (0%)

Query: 12  GKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAGADISEM 71
           G  AV+++N P A N   + +L+E+   +  +  + EV A+++T  G+K F AGAD+   
Sbjct: 22  GHTAVISMNNPPA-NTWTAQSLQELKQKVLALNENKEVYALVITAEGDKFFSAGADLKLF 80

Query: 72  KEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIASSNARFG 131
            + +            + F  L       IAA+NG+A+GGG E+A++CD+RI    A+  
Sbjct: 81  ADGDKQNAADMARYFGEAFETLSTFHGVSIAAINGYAMGGGLEVALACDLRICEEQAQMA 140

Query: 132 QPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVEPSELMNT 191
            PE  +G+ P  GGTQ L+ LVG G AK++I   + I A++A +IGLV +VV      N 
Sbjct: 141 LPEATVGLLPCAGGTQNLTALVGEGWAKRMILCGERINAEKAEKIGLVEEVVVQGNAFNA 200

Query: 192 AKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTEDQKDAMTAFIE 251
           A  +A K+ + +P +VK  KQ +  G        L  E E F   F TEDQ + ++AF+ 
Sbjct: 201 AMALAEKVANQSPSSVKACKQLVQAGRSMPRSQVLPLEREYFANLFDTEDQAEGVSAFLN 260

Query: 252 KRK 254
           KRK
Sbjct: 261 KRK 263


Lambda     K      H
   0.317    0.134    0.365 

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: 151
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: 261
Length of database: 269
Length adjustment: 25
Effective length of query: 236
Effective length of database: 244
Effective search space:    57584
Effective search space used:    57584
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 (21.6 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