GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Herbaspirillum seropedicae SmR1

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate HSERO_RS04630 HSERO_RS04630 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__HerbieS:HSERO_RS04630
          Length = 254

 Score =  248 bits (633), Expect = 9e-71
 Identities = 135/253 (53%), Positives = 170/253 (67%), Gaps = 3/253 (1%)

Query: 7   SVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVT 66
           +VK  V V+TG ASGLG ATAE+L+  GA  VL D+    GE     LG N  F   DVT
Sbjct: 2   AVKQGVYVVTGAASGLGAATAEQLIRAGAKVVLADVNPVAGEKMQATLGANARFVLTDVT 61

Query: 67  SEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTF 126
           SE   Q    +A    G V   VNCAGIA   K   L KG  H L+ F R L++NL+G+F
Sbjct: 62  SETSAQEVFGVASS-MGAVVGLVNCAGIAPGEKL--LGKGGVHRLDSFMRALNINLVGSF 118

Query: 127 NVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDL 186
           N+ RL A  +     D  G+RGVII+TAS+AAF+GQ+GQ AY+ASKGG+V MTLP+AR+L
Sbjct: 119 NMARLAAQHISAGPADATGERGVIIHTASIAAFDGQMGQVAYAASKGGVVSMTLPMAREL 178

Query: 187 APIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFL 246
           A  GIRV+TIAPG+  TP++  +PE+V   L+  VPFP RLG P+E+A LV  I+EN +L
Sbjct: 179 ARHGIRVVTIAPGIIETPMMLGMPEEVLESLSRNVPFPPRLGKPSEFAGLVMHILENRYL 238

Query: 247 NGEVIRLDGAIRM 259
           NGEVIR+DGA+RM
Sbjct: 239 NGEVIRMDGALRM 251


Lambda     K      H
   0.318    0.135    0.385 

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: 204
Number of extensions: 9
Number of successful extensions: 3
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: 254
Length adjustment: 24
Effective length of query: 237
Effective length of database: 230
Effective search space:    54510
Effective search space used:    54510
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 (21.7 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