GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Collimonas arenae Ter10

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate WP_061532312.1 CAter10_RS03585 glutamate-1-semialdehyde 2,1-aminomutase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_001584165.1:WP_061532312.1
          Length = 427

 Score =  151 bits (381), Expect = 4e-41
 Identities = 114/354 (32%), Positives = 166/354 (46%), Gaps = 37/354 (10%)

Query: 1   MNSNKELMQRRSQ-AIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGI 50
           M SN + +  R+Q   P GV             P F  RAE    WD + R Y+D+ G  
Sbjct: 1   MKSNNDTLFARAQLTTPGGVNSPVRAFRSVGGTPRFITRAEGPYFWDADDRRYIDYIGSW 60

Query: 51  AVLNTGHLHPKVVAAVE-AQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVT 109
                GH HP V+ AV+ A  + LS         E   E+C++    VP    ++  LV+
Sbjct: 61  GPAIVGHAHPTVIKAVQDAAARGLSFGAPTQGEIEIAEEICKL----VPS--IEQVRLVS 114

Query: 110 TGSEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKV-----NPYSAGMGLMPG 164
           +G+EA  +A+++AR AT R   + F G YHG     L   G       NP SAG+     
Sbjct: 115 SGTEATMSALRLARGATGRDKIVKFEGCYHGHADSLLVKAGSGLLTFGNPTSAGVP--ED 172

Query: 165 HVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQR 224
            V   L       + + +    +   FKN    + IA +++EPV G      ++P F+Q 
Sbjct: 173 FVKHTL-------VLDYNNTEQLEDAFKNMG--DQIACVIVEPVAGNMNLVRATPEFLQT 223

Query: 225 LRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAE 284
           +R LC ++G +LI DEV  G  R     A    G+APD+T   K I GG P+A   GRA+
Sbjct: 224 MRRLCTQYGAVLIFDEVMCGF-RVALGGAQSLYGIAPDITALGKVIGGGLPVAAFGGRAD 282

Query: 285 VMDAVAPGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGL 335
           +M  +AP G     GT +GNP+A  A +  LK+ ++     +     +KL  GL
Sbjct: 283 LMAHMAPLGSVYQAGTLSGNPVAVAAGMSTLKLIQEPGFYDRLGAQTEKLVGGL 336


Lambda     K      H
   0.320    0.137    0.401 

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: 484
Number of extensions: 32
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: 426
Length of database: 427
Length adjustment: 32
Effective length of query: 394
Effective length of database: 395
Effective search space:   155630
Effective search space used:   155630
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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