GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Nocardioides daejeonensis MJ31

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_110205831.1 DNK54_RS04735 acetylornithine transaminase

Query= BRENDA::Q0K2K2
         (423 letters)



>NCBI__GCF_003194585.1:WP_110205831.1
          Length = 396

 Score =  226 bits (577), Expect = 7e-64
 Identities = 156/408 (38%), Positives = 210/408 (51%), Gaps = 47/408 (11%)

Query: 13  TLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLE 72
           T  TPR V         + E AT+WD +G  Y D   GIAV   GH HP +++A+  QL 
Sbjct: 18  TFGTPRLV-------LAKGEGATVWDADGNEYLDLLGGIAVNLLGHAHPALIEAVTQQLG 70

Query: 73  RFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHTGRPGV 132
              H +         V LAER+ AL+   G  +  L  +G EA E A KI R  TGR  V
Sbjct: 71  TLGHVS-NFFTSGPQVELAERLLALLGQDG--RVFLSNSGTEANEAAFKITR-RTGRTHV 126

Query: 133 IAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLF 192
           +A  G FHGRT+  +ALT K A Y+  F P P D+   P+  A           ALE   
Sbjct: 127 VATEGGFHGRTMGALALTSKAA-YRDPFAPLPGDVTFVPYGDAA----------ALEAAV 175

Query: 193 KTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKM 252
            TD    + AA+++EP+QGE G    P+D++  +R +  +HG ++  DE+QTG GRTG+ 
Sbjct: 176 -TD----QTAAVVLEPIQGEAGVNVPPSDYLARVREITSRHGALMWLDEIQTGVGRTGRW 230

Query: 253 FAMSH-----HDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307
           FA  H       V PDLIT+AK L GG+P+ A     A  D   PG  G T+ GNP+A A
Sbjct: 231 FAHQHPGLAPEPVTPDLITLAKGLGGGLPIGATIALGAAGDLLQPGQHGTTFGGNPVATA 290

Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQ 367
           AA AV+ V EEE L  R+ +LG++LR  L       P ++EVRGLG ++  +        
Sbjct: 291 AALAVLRVAEEESLLARAEALGERLRAGLAD-----PRVSEVRGLGLLIGLDL------- 338

Query: 368 PSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALA 415
            + E +  V   AL AG ++     +   IR   PL +  AQ D  LA
Sbjct: 339 -AQERSAEVAAAALGAGFIINNPTPHR--IRLAPPLVLTDAQADRFLA 383


Lambda     K      H
   0.321    0.136    0.400 

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: 445
Number of extensions: 19
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: 423
Length of database: 396
Length adjustment: 31
Effective length of query: 392
Effective length of database: 365
Effective search space:   143080
Effective search space used:   143080
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 (21.9 bits)
S2: 50 (23.9 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