GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sinorhizobium meliloti 1021

Align Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate SMc00966 SMc00966 acetyl-COA acyltransferase

Query= curated2:Q5HIU0
         (393 letters)



>FitnessBrowser__Smeli:SMc00966
          Length = 397

 Score =  259 bits (662), Expect = 9e-74
 Identities = 161/386 (41%), Positives = 222/386 (57%), Gaps = 14/386 (3%)

Query: 5   VLAAAYRTPIGVFGGAFKDVPAYDLGATLIEHIIKETGLNPSEIDEVIIGNVLQAGQGQN 64
           V+ AA RTP+G   G+   V    L A LIE II +TG++ +EID+V++GN   A    N
Sbjct: 12  VVIAALRTPVGRVNGSLAAVEPARLAALLIERIIADTGIDRAEIDDVLVGNA--ANSAGN 69

Query: 65  PARIAAMKGGLPETVPAFTVNKVCGSGLKSIQLAYQSIVTGENDIVLAGGMENMSQSPML 124
            AR+AA++ GLP  +P  TV++ CGSGL++I LA + I  G     LAGG E+ S++ + 
Sbjct: 70  LARLAALEAGLPVAIPGVTVDRQCGSGLEAIVLAARQIQAGAGRFYLAGGTESASRAHIR 129

Query: 125 VNNSRFGFKMGHQSMVDSMVYDGLTDVFNQYHMGITAENLAEQYGISREEQDTFAVNSQQ 184
           +       +         M  D + D      MG+ AEN+A   GISRE QD FA+ S +
Sbjct: 130 LRPPLTRGEEPQPVKRARMAPDSIGDP----DMGVAAENVATACGISRERQDRFALESHR 185

Query: 185 KAVRAQQNGEFDSEIVPVSIPQRKGEPIVVTKDEGVRENVSVEKLSRLRPAFKKDGTVTA 244
           +AV A+  G F  EIVPV  P+       + +DE  R N S E LSRLRP F   GTVTA
Sbjct: 186 RAVAAEAEGRFSREIVPVPTPEGP-----IARDECPRANASAETLSRLRPVFVAGGTVTA 240

Query: 245 GNASGINDGAAMMLVMSEDKAKELNIEPLAVLDGFGSHGVDPSIMGIAPVGAVEKALKRS 304
           GNA  +NDGAAM+L+ +  +A++L            + GV+P ++G+ PV A+ K   R+
Sbjct: 241 GNACPVNDGAAMVLMTNLAEARKLGTRFGLAFTDAATAGVEPKLLGLGPVPAMAKLRARN 300

Query: 305 KK-ELSDIDVFELNEAFAAQSLAVDRELKLPPEKVNVKGGAIALGHPIGASGARVLVTLL 363
              +++ +D  E NEAFA+Q L    +L + PE+VN  GGAIALGHP GASGA ++V L 
Sbjct: 301 PALDVARVDFIEFNEAFASQVLGSLDQLDIAPERVNRDGGAIALGHPYGASGAILVVRLF 360

Query: 364 HQL--NDEVETGLTSLCIGGGQAIAA 387
            Q+        GL  + IGGG  IAA
Sbjct: 361 SQMLAASSPAEGLAMMGIGGGMGIAA 386


Lambda     K      H
   0.314    0.133    0.368 

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: 406
Number of extensions: 19
Number of successful extensions: 6
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: 393
Length of database: 397
Length adjustment: 31
Effective length of query: 362
Effective length of database: 366
Effective search space:   132492
Effective search space used:   132492
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: 42 (22.0 bits)
S2: 50 (23.9 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