GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Desulfoscipio geothermicus DSM 3669

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_245779653.1 BM299_RS04985 aspartate aminotransferase family protein

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_900115975.1:WP_245779653.1
          Length = 471

 Score =  204 bits (520), Expect = 3e-57
 Identities = 134/403 (33%), Positives = 207/403 (51%), Gaps = 37/403 (9%)

Query: 29  VRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHV--SNVFTNEPA 86
           VR EG+RVWD  G   +DF GG    ++GH HP +++A+ EQ + + ++  +++ T   A
Sbjct: 55  VRAEGTRVWDSEGNAYLDFLGGYGSLNIGHNHPRVIEAV-EQVRELPNILQASIPTITAA 113

Query: 87  LRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTL 146
           L     ++     +R FL NSGAEA E A KLAR          +   I   NSFHG++ 
Sbjct: 114 LLHNLAVITPGKLKRSFLCNSGAEAVEGALKLARAATG------RKTFIYCRNSFHGKSF 167

Query: 147 FTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISD-KTCAVVLEPIQGEGGVLPAQ 205
             ++V G+ KY + F P       VP+ D++AL+ A+   +  A ++EP+QGEGG+    
Sbjct: 168 GALSVTGREKYRELFEPLLFDCREVPFGDIDALRKALRKYQAAAFIVEPVQGEGGINMPP 227

Query: 206 QAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGG-FPIG 264
           + YL  A + C +   L + DE+Q+G GR G +FA  H  V PD++  AKSLGGG  PIG
Sbjct: 228 RGYLSEAARACRDAGTLFIADEIQTGFGRTGAMFACQHENVEPDVMCLAKSLGGGIMPIG 287

Query: 265 AMLTTGEIAKHL-----SVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFK 319
           A +T  +I +           H +T+GGN  A+A   AA++V+   ++      K   F 
Sbjct: 288 AFITNDDIWQKAYGSVEKATLHTSTFGGNTWAAAAGIAAIEVLVKEKLPAAAAEKGTYFI 347

Query: 320 SRLQKIGQEYGIFDEIRGMGLLIG------------------AALTDEWKGK--ARDVLN 359
           S L+ + ++Y +  E+RG GLLIG                  + L+ E+ G   A ++LN
Sbjct: 348 SGLRDLQKKYPLLQEVRGQGLLIGIELAQPGGLTNKATMGLASKLSHEYLGSMVAGELLN 407

Query: 360 AAEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAK 402
                    L  +P+V+R  P L +   E+D  L   +  + K
Sbjct: 408 RHRIITAYTLN-NPNVIRMEPPLTVTGEELDYVLNALDDVLKK 449


Lambda     K      H
   0.318    0.135    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: 458
Number of extensions: 27
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: 406
Length of database: 471
Length adjustment: 32
Effective length of query: 374
Effective length of database: 439
Effective search space:   164186
Effective search space used:   164186
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: 41 (21.7 bits)
S2: 51 (24.3 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