GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sphingomonas koreensis DSMZ 15582

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Korea:Ga0059261_3205
          Length = 398

 Score =  195 bits (496), Expect = 2e-54
 Identities = 143/405 (35%), Positives = 190/405 (46%), Gaps = 41/405 (10%)

Query: 24  CDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVP 83
           C+    R E   L    G  Y DFAAGIAV   GH HP+  +AIA Q     H +     
Sbjct: 13  CEVRPVRGEGCYLIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAATLMHVSNLYGS 72

Query: 84  YQGYVTLAERINALVPIQGLNKTALFT-TGAEAVENAIKIARAH---TGRPG---VIAFS 136
            QG   LA+RI           T  FT +G EA+E AIK AR +    G P    +I F 
Sbjct: 73  PQGEA-LAQRIVD----NSFADTVFFTNSGVEAIECAIKTARRYHYVNGNPQRHKLITFK 127

Query: 137 GAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDI 196
            AFHGR++  ++ T +    + GF P      +  F               LEG      
Sbjct: 128 NAFHGRSIGAISATDQ-PKMRDGFEPLLPGFDYVKFND-------------LEGAIAKID 173

Query: 197 DPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMS 256
           D    A  +VE VQGEGG  A   +F++GLR  CD+HG++LI DE+Q G+GRTGKM+A  
Sbjct: 174 D--ETAGFLVETVQGEGGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYE 231

Query: 257 HHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVI 316
           H+ + PD++T AK +  G PL A             G  G TY GNPLA+AA  AV+DV+
Sbjct: 232 HYGITPDILTAAKGIGNGFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMAAGQAVLDVM 291

Query: 317 EEEKLCERSASLGQQLR---EHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHA 373
            E    E    +G++LR   E L+    H     E+RG G M+  +  +PA  +    H 
Sbjct: 292 LEPGFFEHVEKMGERLRAGFEQLIPNHDH--LFDEIRGKGLMLGIKLKEPAVSRDFVAH- 348

Query: 374 KRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLT 418
                  L     LLT     NV R L PL I ++     +  L+
Sbjct: 349 -------LRENHGLLTVAAGENVFRVLPPLVIEESHIAECIEKLS 386


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: 456
Number of extensions: 28
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: 398
Length adjustment: 31
Effective length of query: 392
Effective length of database: 367
Effective search space:   143864
Effective search space used:   143864
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 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