GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Novosphingobium barchaimii LL02

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_059150767.1 V474_RS04200 crotonase/enoyl-CoA hydratase family protein

Query= CharProtDB::CH_091794
         (261 letters)



>NCBI__GCF_001046635.1:WP_059150767.1
          Length = 267

 Score =  151 bits (382), Expect = 1e-41
 Identities = 95/260 (36%), Positives = 145/260 (55%), Gaps = 10/260 (3%)

Query: 6   VILEKEGK-VAVVTINRPKALNALNS-DTLKEMDYVIGEIENDSEVLAVILTGAGEKSFV 63
           V+ E + K + ++T+NRP   N ++  + ++ +   +  +E D      ILTGAG K F 
Sbjct: 5   VLYEIDDKGIVLLTLNRPALRNPISDPEVIEALLAALAYLEADPAARVAILTGAG-KGFS 63

Query: 64  AGADISEMKEMNTIEGRKFGILG---NKVFRRLEL----LEKPVIAAVNGFALGGGCEIA 116
           +G DI++MK    +      +      +  +RL L    LE PVIAAVNG A+G GC++ 
Sbjct: 64  SGGDINQMKPGGNLNSGSPAVTRLNYKRGIQRLPLAFAALEVPVIAAVNGAAMGAGCDLT 123

Query: 117 MSCDIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRI 176
             CD+RIA  +A+F +  V LG+  G GG+  L R+VG   A ++  T   I A EAL  
Sbjct: 124 CMCDLRIAGESAKFAESFVKLGLIAGDGGSWLLPRVVGWSKAAEMALTGDPIDAAEALAC 183

Query: 177 GLVNKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGEC 236
           GLV++VV   ELMN A+ +A +I  N P AV+++K+ +  G + D+ + L   S      
Sbjct: 184 GLVSRVVPDGELMNAARALALRIAVNPPHAVRMTKRLLWEGRRADLASLLEMASAMQAAA 243

Query: 237 FSTEDQKDAMTAFIEKRKIE 256
            +T D  +A+TAF+EKR  E
Sbjct: 244 HATADHAEAVTAFLEKRPPE 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: 186
Number of extensions: 10
Number of successful extensions: 1
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: 267
Length adjustment: 25
Effective length of query: 236
Effective length of database: 242
Effective search space:    57112
Effective search space used:    57112
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