GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Xanthobacter autotrophicus Py2

Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39; 4-hydroxy-2-keto-pentanoic acid aldolase; 4-hydroxy-2-oxopentanoate aldolase (uncharacterized)
to candidate WP_012113349.1 XAUT_RS06660 2-isopropylmalate synthase

Query= curated2:B1VRH5
         (340 letters)



>NCBI__GCF_000017645.1:WP_012113349.1
          Length = 527

 Score = 65.1 bits (157), Expect = 4e-15
 Identities = 74/286 (25%), Positives = 113/286 (39%), Gaps = 45/286 (15%)

Query: 3   QVVIHDPTLRDGQHAVHHRLGLTELRRYAEAADAARVPVVEVGHGNGLGASSLQVGLAAA 62
           +VVI D TLRDG+      +   E    A   D   V V+E G             +A+ 
Sbjct: 19  RVVIFDTTLRDGEQCPGASMTFEEKLEVAALLDEMGVDVIEAGFP-----------IASI 67

Query: 63  TDDAMLSTVREALRHSRLGTFMLPGWGTSDDLRRAISHGVDVFRVGVHATEASLAEHHLG 122
            D   ++ +    +++ +           D    A+ H     R G   T  S +  H+ 
Sbjct: 68  GDFESVAEIARRTQNATVAGLSRAALNDIDRCAEAVKHA----RRGRIHTFLSTSPVHMK 123

Query: 123 FLRDAGAEAHCVLMM---------SHMASPGELAEQAAR------------AVGYGAQAV 161
           +      + H VL M         +H+      +E   R            A+  GA  +
Sbjct: 124 YKLQK--QPHEVLEMVVASVTRARNHVEDVEWSSEDGTRTEIDFLCRCVEAAIKAGATTI 181

Query: 162 GIMDSAGHFLPPDVTARIGAIVEAV-GTVPVIF--HGHNNLGMAVANSVAAAEAGARIID 218
            I D+ G+  P +  A    ++E V  +   IF  H H++LGMAVANS+A    GAR I+
Sbjct: 182 NIPDTVGYTTPAEYEALFRTVIERVPNSDKAIFSVHCHDDLGMAVANSLAGLAGGARQIE 241

Query: 219 GCARGFGAGAGNTQLEVLVPVLERSG----FATGIDLYALLDAADL 260
               G G  AGN  LE +V  +E       + +GI+   L  A+ L
Sbjct: 242 CTVNGIGERAGNAALEEVVMAIETRSDVLPYRSGINTKMLTRASKL 287


Lambda     K      H
   0.320    0.135    0.393 

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: 320
Number of extensions: 10
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 340
Length of database: 527
Length adjustment: 32
Effective length of query: 308
Effective length of database: 495
Effective search space:   152460
Effective search space used:   152460
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 (21.8 bits)
S2: 50 (23.9 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