GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kbl in Azospirillum brasilense Sp245

Align 2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial; AKB ligase; Aminoacetone synthase; Glycine acetyltransferase; EC 2.3.1.29 (characterized)
to candidate AZOBR_RS03625 AZOBR_RS03625 5-aminolevulinate synthase

Query= SwissProt::O75600
         (419 letters)



>FitnessBrowser__azobra:AZOBR_RS03625
          Length = 404

 Score =  235 bits (599), Expect = 2e-66
 Identities = 131/345 (37%), Positives = 197/345 (57%), Gaps = 4/345 (1%)

Query: 70  FCANNYLGLSSHPEVIQAGLQALEEFGAGLSSVRFICGTQSIHKNLEAKIARFHQREDAI 129
           +C+N+YLG+  +P V++A   A++  GAG    R I GT   H  LE ++A  HQ+E A+
Sbjct: 51  WCSNDYLGMGQNPVVLKAMHDAIDGVGAGAGGTRNISGTNIYHVLLERELADLHQKEAAL 110

Query: 130 LYPSCYDANAGLFEAL--LTPEDAVLSDELNHASIIDGIRLCKAHKYRYRHLDMADLEAK 187
           L+ S Y +N      L  L P   +LSD LNH S+I GIR   A K+ +RH D   L+  
Sbjct: 111 LFTSGYVSNDATLGTLGKLLPNCVILSDALNHNSMITGIRNSGAEKHIFRHNDPKHLDEL 170

Query: 188 LQEAQKHRLRLVATDGAFSMDGDIAPLQEICCLASRYGALVFMDECHATGFLGPTGRGTD 247
           L +    R ++VA +  +SMDGD+AP+ ++C +A ++GA+ ++DE HA G  GP G G  
Sbjct: 171 LSQIAPDRPKVVAFESVYSMDGDVAPIHDLCDVADKHGAMTYLDEVHAVGMYGPRGGGVA 230

Query: 248 ELLGVMDQVTIINSTLGKALGGASGGYTTGPGPLVSLLRQRARPYLFSNSLPPAVVGCAS 307
           E  G MD++TII  TLGKA  G  GGY TG   LV  +R  A  ++FS SL P +   A 
Sbjct: 231 ERDGAMDRLTIIEGTLGKAF-GVQGGYITGSTALVDCIRSFAAGFIFSTSLSPVLAAGAL 289

Query: 308 KALDLLMGSNTIVQSMAAKTQRFRSKMEAAGFTISGASHPICPVMLGDARLASRMADDML 367
            ++  L  S T       +    +  M  AG  +  ++  I PVM+GDA    R +D+++
Sbjct: 290 ASIRYLKTSQTERDQHQERAATLKRLMAEAGLPVMPSASHIVPVMVGDAHRCKRASDELM 349

Query: 368 KR-GIFVIGFSYPVVPKGKARIRVQISAVHSEEDIDRCVEAFVEV 411
           +R  I+V   +YP VP+G  R+R   + +HS+ ++ R V+A ++V
Sbjct: 350 ERHDIYVQPINYPTVPRGGERLRFTPTPLHSDAEMARLVDALLDV 394


Lambda     K      H
   0.322    0.137    0.414 

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: 375
Number of extensions: 23
Number of successful extensions: 4
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: 419
Length of database: 404
Length adjustment: 31
Effective length of query: 388
Effective length of database: 373
Effective search space:   144724
Effective search space used:   144724
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 (21.9 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