GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Paraburkholderia bryophila 376MFSha3.1

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_03178 H281DRAFT_03178 succinate semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__Burk376:H281DRAFT_03178
          Length = 486

 Score =  248 bits (633), Expect = 3e-70
 Identities = 157/446 (35%), Positives = 242/446 (54%), Gaps = 7/446 (1%)

Query: 14  ADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQVLFRFKQ 73
           AD G T +V NP+TGE V  VP       ++AIDAA AA+PAWR +   +RA +L ++  
Sbjct: 25  ADDGSTFEVVNPATGEVVATVPRMGTAETRRAIDAANAAWPAWRASTAKQRAVILRKWHD 84

Query: 74  LLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRNVGPNIDAW 133
           L+  N + +  +++ E GK + +A GE++     +E+     + L G+       +    
Sbjct: 85  LMLENADDLALILTTEQGKPLAEAKGEIQYAASFLEWFAEEGKRLNGDTIPTPANDKRIV 144

Query: 134 SDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIAELFHEAGL 193
              +P+GV A ITP+NFPA +       A+A G   I+KP+E  P S L +A L   AG+
Sbjct: 145 VTKEPVGVCAAITPWNFPAAMITRKVGPALAAGCPIIVKPAEATPLSALALAVLAERAGV 204

Query: 194 PKGVLNVVHGDKGAVDA-LIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQALGGAKNH 252
           P+GV NVV G+  A+ A +   P V+ LSF GSTP+   + ++     K+V    G    
Sbjct: 205 PRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPVGRLLMAQCAPTVKKVSLELGGNAP 264

Query: 253 AVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQIKGLKIGA 312
            ++  DADLD AV+  + + Y + G+ C+  +    V D++ DA   KL   ++ L +G 
Sbjct: 265 FIVFDDADLDAAVAGAIASKYRNSGQTCVCTN-RFYVHDKVYDAFAAKLRAAVEQLTVGR 323

Query: 313 GTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFLGGTLFDRV 372
           GT  G+  GPL+  AA  KV  +I+  +A+GA +V  G+ + + GH  GFF    L D V
Sbjct: 324 GTEAGVTQGPLINEAAVLKVESHIEDALAKGARVVTGGKRHAL-GH--GFFEPTILAD-V 379

Query: 373 TPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVG 432
           TP+M + ++E FGP+  + R +S EE + L ND E+G  +  ++RD        + +E G
Sbjct: 380 TPDMKVARDETFGPLAPLFRFSSDEEVIALANDTEFGLASYFYSRDIGRVWRVAEALEYG 439

Query: 433 MVGVNVPLPVPVAYHSFGGWKRSLFG 458
           MVG+N  L +      FGG K+S  G
Sbjct: 440 MVGINTGL-ISNEVAPFGGVKQSGLG 464


Lambda     K      H
   0.319    0.137    0.411 

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: 607
Number of extensions: 33
Number of successful extensions: 5
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: 498
Length of database: 486
Length adjustment: 34
Effective length of query: 464
Effective length of database: 452
Effective search space:   209728
Effective search space used:   209728
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 (21.7 bits)
S2: 52 (24.6 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