GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Rhizobium etli CFN 42

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase

Query= CharProtDB::CH_091794
         (261 letters)



>NCBI__GCF_000092045.1:WP_042119745.1
          Length = 260

 Score =  126 bits (316), Expect = 5e-34
 Identities = 83/248 (33%), Positives = 127/248 (51%), Gaps = 7/248 (2%)

Query: 10  KEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAGADIS 69
           ++G V  V I+RPKA NA++  T + M  +  +  +D E+   I++GAGEK F AG D+ 
Sbjct: 9   RDGAVLEVVIDRPKA-NAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKFFCAGWDLK 67

Query: 70  EMKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIASSNAR 129
                + ++G  +G+ G    + L  L KPVI AVNG   GGG EIA+S D+ IA+ +A 
Sbjct: 68  AAASGDAVDG-DYGVGGFGGLQELRDLNKPVICAVNGLCCGGGLEIALSTDLIIAAEHAT 126

Query: 130 FGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVEPSELM 189
           F  PE+  G T     + +L + +   +A  ++ T + +   EA R G VN+VV    LM
Sbjct: 127 FALPEIRSG-TVADAASIKLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVPAERLM 185

Query: 190 NTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTAL----AFESEAFGECFSTEDQKDA 245
             A E+A  + S  P+     K+ +         TA+      +       +S+EDQ + 
Sbjct: 186 ERAWELARLLESGPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSEDQLEG 245

Query: 246 MTAFIEKR 253
             AF EKR
Sbjct: 246 ARAFAEKR 253


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: 144
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: 261
Length of database: 260
Length adjustment: 25
Effective length of query: 236
Effective length of database: 235
Effective search space:    55460
Effective search space used:    55460
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 Apr 09 2024. 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