GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Azospirillum brasilense Sp245

Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate AZOBR_RS14060 AZOBR_RS14060 malate dehydrogenase

Query= BRENDA::Q8I8U5
         (330 letters)



>FitnessBrowser__azobra:AZOBR_RS14060
          Length = 322

 Score =  343 bits (879), Expect = 4e-99
 Identities = 176/322 (54%), Positives = 229/322 (71%), Gaps = 5/322 (1%)

Query: 9   RPKIAMVGSGMIGGTMAFLCSLRELGDVVLFDVVPNMPMGKAMDISHNSSVVDTGITVYG 68
           R KIA+VG+G IGGT+A L + +ELGDVVLFD+   MP GKA+D++  S V      + G
Sbjct: 3   RKKIALVGAGQIGGTLALLAAQKELGDVVLFDIAEGMPEGKALDLAETSPVEGFNAKLSG 62

Query: 69  SNSYECLKGADVVIITAGITKIPGKSDKEWSRMDLLPVNIKIMREVGAAIKSYCPNAFVI 128
            N Y  ++GADVVI+TAG+ + PG S     R DL+ +N  + + VG  IK Y PNAFVI
Sbjct: 63  GNDYSVIEGADVVIVTAGVPRKPGMS-----RDDLIGINTGVCQTVGENIKKYAPNAFVI 117

Query: 129 NITNPLDVMVAALQESSGLPHHRICGMAGMLDSSRFRRMIADKLEVSPRDVQGMVIGVHG 188
            ITNPLDVMV  LQ++SGLP  R+ GMAG+LDS+RFR  +AD+ +VS  DV   V+G HG
Sbjct: 118 VITNPLDVMVWVLQQASGLPPERVVGMAGVLDSARFRYFLADEFKVSVEDVTAFVLGGHG 177

Query: 189 DHMVPLSRYATVNGIPLSEFVKKGWIKQEEVDDIVQKTKVAGGEIVRLLGQGSAYYAPGA 248
           D MVPL RY+TV GIPL + VK GW  QE++D IVQ+T+  G EIV+LL  GSA+YAP A
Sbjct: 178 DTMVPLVRYSTVAGIPLPDLVKMGWTTQEKLDAIVQRTRDGGAEIVKLLKTGSAFYAPAA 237

Query: 249 SAIQMAESYLKDRKRVMVCSCYLQGQYGVQNHYLGVPCVIGGRGVEKIIELELTAQERQE 308
           SAIQMAESYLKD+KRV+  + YL GQYG  + Y+GVP +IG  GVEKIIE++L+A+E++ 
Sbjct: 238 SAIQMAESYLKDQKRVVPVAAYLTGQYGQNDLYVGVPTIIGAGGVEKIIEIDLSAEEKKM 297

Query: 309 LQGSIDEVKEMQKAIAALDASK 330
              S+D VK++ + +    A K
Sbjct: 298 FDHSVDAVKQLVEVVKKQQAEK 319


Lambda     K      H
   0.319    0.136    0.394 

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: 339
Number of extensions: 15
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: 330
Length of database: 322
Length adjustment: 28
Effective length of query: 302
Effective length of database: 294
Effective search space:    88788
Effective search space used:    88788
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: 48 (23.1 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