GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Escherichia coli BW25113

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Keio:15866
          Length = 406

 Score =  217 bits (552), Expect = 6e-61
 Identities = 143/397 (36%), Positives = 204/397 (51%), Gaps = 37/397 (9%)

Query: 26  FYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPYQ 85
           F   R E + LWD +G+ Y DFA GIAV   GH HP + +A+  Q  +F HT        
Sbjct: 23  FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTG------N 76

Query: 86  GYVT--LAERINALVPIQGLNKTALFTTGAEAVENAIKIAR--AH----TGRPGVIAFSG 137
           GY    +      L+     ++     +GAEA E A+K+AR  AH    + + G++AF  
Sbjct: 77  GYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKN 136

Query: 138 AFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDID 197
           AFHGRTL  ++  G+ A Y   F P P+DI HA    A + +++  AL          ID
Sbjct: 137 AFHGRTLFTVSAGGQPA-YSQDFAPLPADIRHA----AYNDINSASAL----------ID 181

Query: 198 PARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSH 257
            +   A+IVEP+QGEGG   A   F++GLR +C++H  +LI DEVQTG GRTG+++A  H
Sbjct: 182 DS-TCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMH 240

Query: 258 HDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIE 317
           + V PDL+T AK+L GG P+ A+            G  G TY GNPLA A A  V+++I 
Sbjct: 241 YGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELIN 300

Query: 318 EEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQ 377
             ++            E L          +EVRGLG ++         GQ     AK++ 
Sbjct: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQ-----AKQIS 355

Query: 378 TRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAAL 414
             A +AG+++L  G  GNV+RF   L + + +    L
Sbjct: 356 QEAAKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGL 390


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: 454
Number of extensions: 27
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: 423
Length of database: 406
Length adjustment: 31
Effective length of query: 392
Effective length of database: 375
Effective search space:   147000
Effective search space used:   147000
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