GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Cupriavidus basilensis 4G11

Align 4-aminobutyrate aminotransferase GabT; (S)-3-amino-2-methylpropionate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.22 (characterized)
to candidate RR42_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Cup4G11:RR42_RS21370
          Length = 420

 Score =  488 bits (1257), Expect = e-142
 Identities = 242/415 (58%), Positives = 309/415 (74%), Gaps = 2/415 (0%)

Query: 4   NKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVV 63
           N EL++R+  A PRGVG +   FA+RAEN  +WDVEG+ Y+DFA GIAVLNTGH HP++V
Sbjct: 3   NAELVRRKDAATPRGVGVMCNFFAERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPRLV 62

Query: 64  AAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR 123
            A++ QL++ +HT +Q++ Y  Y+EL E +NQ+ PG  AKKT   TTG+EAVENA+KIAR
Sbjct: 63  EAMQRQLERFTHTAYQIVPYASYIELAERINQRAPGRGAKKTAFFTTGAEAVENAIKIAR 122

Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDA 183
           AAT R G IAFSG +HGRT   +ALTGKV PY  G G  PG V+ A YPC LHG+S +DA
Sbjct: 123 AATGRPGVIAFSGGFHGRTMMGMALTGKVVPYKVGFGPFPGEVFHAPYPCALHGVSVEDA 182

Query: 184 IASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQS 243
           + ++  +FK D  P+ +AAI+ EPVQGEGGF  + PAF++ LRA+CDEHGI+L+ADEVQ+
Sbjct: 183 LKAMEHLFKADVDPKRVAAIIFEPVQGEGGFNVAPPAFVKALRAICDEHGILLVADEVQT 242

Query: 244 GAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPI 303
           G GRTG LFAME   VAPDLTT AKS+AGG PL+ V GRAEVMDA APGGLGGTYAGNP+
Sbjct: 243 GFGRTGKLFAMEHYDVAPDLTTMAKSLAGGMPLSAVCGRAEVMDAPAPGGLGGTYAGNPL 302

Query: 304 ACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDG 363
           A  +AL VL V E E L+ +   LGQ+L   L A+  + P+I ++RGLGAM+A+E F   
Sbjct: 303 AVASALAVLDVLEGEQLIPRGAALGQRLVARLEALKARVPQIAEIRGLGAMVAVE-FRRA 361

Query: 364 DHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIIS 418
           D   PDA+ T E+  RA ++GL+LLSCG Y NV+R L PLTI DA + +GL+I++
Sbjct: 362 D-GAPDAEFTREVQNRALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILA 415


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: 597
Number of extensions: 23
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: 426
Length of database: 420
Length adjustment: 32
Effective length of query: 394
Effective length of database: 388
Effective search space:   152872
Effective search space used:   152872
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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