GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Pseudomonas putida KT2440

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate PP_4223 PP_4223 diaminobutyrate-2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Putida:PP_4223
          Length = 452

 Score =  200 bits (508), Expect = 8e-56
 Identities = 144/434 (33%), Positives = 215/434 (49%), Gaps = 34/434 (7%)

Query: 3   SNKELMQRRSQ------AIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTG 56
           ++  L+QR+ Q      + PR +    P+   RA    V DVEGR+++D   G   L  G
Sbjct: 9   TDSPLLQRQQQQESNARSYPRRI----PLALRRARGIHVEDVEGRQFIDCLAGAGTLALG 64

Query: 57  HLHPKVVAAVEAQL--KKLSHTCFQVLAYEPYL--ELCEIMNQKVPGDFAKKTLLVTTGS 112
           H HP VV A++  L  +   HT       +     +L  I+ + +  + AK      TG+
Sbjct: 65  HNHPVVVEAIQRVLADELPLHTLDLTTPVKDRFVQDLFGILPEALRRE-AKVQFCGPTGT 123

Query: 113 EAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYP 172
           +AVE A+K+ R AT RS  +AF GAYHG +   L L G   P      L+   V    YP
Sbjct: 124 DAVEAALKLVRTATGRSTVLAFQGAYHGMSQGALNLMGSHGPKQPLGALLGNGVQFMPYP 183

Query: 173 ----CPLHGISEDDAIASIHRIFKNDAAPED----IAAIVIEPVQGEGGFYASSPAFMQR 224
               CP     E    A++H +      PE      AA+++E VQGEGG   +   +++ 
Sbjct: 184 YDYRCPFGLGGEAGVKANLHYLENLLLDPESGVPLPAAVILEVVQGEGGVVPADIEWLKG 243

Query: 225 LRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAE 284
           +R + ++ G+ LI DE+QSG  RTG +FA E  G+ PD+ T +K+I G  PLA V  R +
Sbjct: 244 VRRITEQAGVALIVDEIQSGFARTGRMFAFEHAGIVPDVVTLSKAIGGSLPLAVVVYR-D 302

Query: 285 VMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPE 344
            +D   PG   GT+ GN +A  A   V+    +  L + A  +GQ+L+  L  +   +P+
Sbjct: 303 WLDTWKPGAHAGTFRGNQMAMAAGSAVINYLVEHRLAEHAEAMGQRLRGHLQRLQRDYPQ 362

Query: 345 IGDVRGLGAMIAIELFEDGDHNKPDA--------KLTAEIVARARDKGLILLSCGPYYNV 396
           +GD+RG G M+ +EL +     +PDA         L  ++      +GLIL   G +  V
Sbjct: 363 LGDIRGRGLMLGVELVD--PQGQPDALGHPPANRDLAPKVQRECLKRGLILELGGRHGAV 420

Query: 397 LRILVPLTIEDAQI 410
           +R L PL I   QI
Sbjct: 421 VRFLPPLIISAEQI 434


Lambda     K      H
   0.320    0.137    0.401 

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: 500
Number of extensions: 16
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: 426
Length of database: 452
Length adjustment: 32
Effective length of query: 394
Effective length of database: 420
Effective search space:   165480
Effective search space used:   165480
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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