GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Marinobacter adhaerens HP15

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate GFF2748 HP15_2692 phenylacetate degradation probable enoyl-CoA hydratase paaB

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



>FitnessBrowser__Marino:GFF2748
          Length = 263

 Score =  156 bits (394), Expect = 5e-43
 Identities = 91/263 (34%), Positives = 142/263 (53%), Gaps = 6/263 (2%)

Query: 1   MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKA 60
           MT  ++L++I + VAL+TLNRP  LN+ N ++   + +A+  +  D  +  +V+TGS + 
Sbjct: 1   MTQPSILLEIDQGVALLTLNRPDNLNSFNVEMHERMREAISTVRKDESVRVLVITGSGRG 60

Query: 61  FAAGADIKEMA-----ELTYPQIYLDDFFADADR-IATRRKPLIAAVAGYALGGGCELAL 114
           F AG D+ + +     E+      L++++    R +     P++ AV G A G G  +AL
Sbjct: 61  FCAGQDLSDRSVSPDQEMPDLGASLENYYNPLMRSLRDLPMPVLCAVNGVAAGAGANIAL 120

Query: 115 LCDMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAG 174
            CD+  AA +A F Q    LG++P  GGT  L R  G A+A  M L G ++ A +AE  G
Sbjct: 121 ACDITLAARSANFVQAFCKLGLVPDSGGTWTLPRVAGMARAKGMALLGDKISAEQAENWG 180

Query: 175 LVARVFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVF 234
           ++ R    E L+EET+K AR  A +      +IK +++ +   T  E I  ER +     
Sbjct: 181 MIWRCVDNEQLMEETMKLARHFATQPTKGLALIKRALHASASNTFEEQINLERDLQRMAG 240

Query: 235 ATADQKEGMAAFSEKRKPEFTNR 257
            T D +EG+AAF EKR P F  +
Sbjct: 241 QTEDYREGVAAFMEKRTPNFKGK 263


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: 115
Number of extensions: 3
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: 263
Length adjustment: 24
Effective length of query: 233
Effective length of database: 239
Effective search space:    55687
Effective search space used:    55687
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