GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Cupriavidus basilensis 4G11

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate RR42_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__Cup4G11:RR42_RS21370
          Length = 420

 Score =  264 bits (675), Expect = 4e-75
 Identities = 154/406 (37%), Positives = 230/406 (56%), Gaps = 20/406 (4%)

Query: 41  ERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAI 100
           ER E   ++DV+G  + DFA+G+ V+N GH HPR+VEA+++Q E+FTH +     Y + I
Sbjct: 27  ERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPRLVEAMQRQLERFTHTAYQIVPYASYI 86

Query: 101 ILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLS 160
            LAE++ + APG   +K  +  +GAEA E A+K+ +  TGR   +AF   FHGRT   ++
Sbjct: 87  ELAERINQRAPGRGAKKTAFFTTGAEAVENAIKIARAATGRPGVIAFSGGFHGRTMMGMA 146

Query: 161 LTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFR-HV 219
           LT      + GF P    V H PYP        + G    D L         E++F+  V
Sbjct: 147 LTGKVVPYKVGFGPFPGEVFHAPYP------CALHGVSVEDALK------AMEHLFKADV 194

Query: 220 PPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIE 279
            P  + AI FEP+QGEGG+ V P  F KAL+   DE+GILL  DEVQ G GRTGK +A+E
Sbjct: 195 DPKRVAAIIFEPVQGEGGFNVAPPAFVKALRAICDEHGILLVADEVQTGFGRTGKLFAME 254

Query: 280 HFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIV 338
           H+ V PDL    K++ GG+PL+ V  RA++     PG    T+ GNP+A+A+ + V++++
Sbjct: 255 HYDVAPDLTTMAKSLAGGMPLSAVCGRAEVMDAPAPGGLGGTYAGNPLAVASALAVLDVL 314

Query: 339 --KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDR 396
             ++L+P    +G  L   LE  K +   I + RGLG   AVE  ++    +   E    
Sbjct: 315 EGEQLIPRGAALGQRLVARLEALKARVPQIAEIRGLGAMVAVEFRRADGAPD--AEFTRE 372

Query: 397 IVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEAL 440
           +   + ++GL+LL CG   N IRF+ PL ++   ++  ++I  + L
Sbjct: 373 VQNRALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILADVL 418


Lambda     K      H
   0.320    0.141    0.418 

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: 501
Number of extensions: 28
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: 445
Length of database: 420
Length adjustment: 32
Effective length of query: 413
Effective length of database: 388
Effective search space:   160244
Effective search space used:   160244
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 (21.7 bits)
S2: 51 (24.3 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