GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD 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_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__Cup4G11:RR42_RS26240
          Length = 420

 Score =  271 bits (694), Expect = 2e-77
 Identities = 156/405 (38%), Positives = 230/405 (56%), Gaps = 18/405 (4%)

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

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

Query: 161 LTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVP 220
           LT      + GF P    V H PYP      +G+ G    D      ++ + +     V 
Sbjct: 147 LTGKVVPYKVGFGPFPGDVFHAPYP------YGLHGVSVQDS-----INALHQLFKADVD 195

Query: 221 PHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEH 280
           P  + AI FEP+QGEGG+ V P  F +AL+   DE+GILL  DEVQ G GRTGK +A+EH
Sbjct: 196 PKRVAAIIFEPVQGEGGFNVAPAEFVRALRAICDEHGILLVADEVQTGFGRTGKLFAMEH 255

Query: 281 FGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIV- 338
           + V PDL    K++ GG+PL+ V  RA+I     PG    T+ GNP+A+A+ + V++++ 
Sbjct: 256 YDVTPDLTTMAKSLAGGMPLSAVCGRAEIMDAPAPGGLGGTYAGNPLAVASALAVLDVLE 315

Query: 339 -KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRI 397
            ++L+     +G  L   L+  K +   IG+ RG+G   AVE  K+    +  PE   ++
Sbjct: 316 SEKLIERGAALGQRLQDKLDGLKSRVPEIGEVRGVGAMIAVEFRKADGRPD--PEFTRQV 373

Query: 398 VKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEAL 440
              + +RGL+LL CG   N +RF+ PL +    +D  + I E AL
Sbjct: 374 QDRALERGLLLLSCGVYGNVVRFLFPLTIPDAVMDEGLGILEAAL 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: 530
Number of extensions: 35
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: 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