GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Herbaspirillum seropedicae SmR1

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase

Query= SwissProt::P50457
         (421 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05420 HSERO_RS05420
           4-aminobutyrate aminotransferase
          Length = 426

 Score =  588 bits (1515), Expect = e-172
 Identities = 288/418 (68%), Positives = 343/418 (82%)

Query: 2   SNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDL 61
           +N E  QR+ +ATPRGVGVMC+F+A+ A NA L DVEG  +IDFAAGIAVLNTGHRHP L
Sbjct: 6   NNQELQQRKNAATPRGVGVMCDFYAERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKL 65

Query: 62  VAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIA 121
           + A+  Q+ +FTHTAYQIVPY SYV LAE+IN L P +   KTAFF+TGAEAVENA+KIA
Sbjct: 66  LDAMRAQMDKFTHTAYQIVPYASYVELAERINRLTPGNYPKKTAFFSTGAEAVENAIKIA 125

Query: 122 RAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQD 181
           RAHTGRPGVIAF+GGFHGRT M MALTGKVAPYK+GFGPFPG V+H PYPS LHGI+++D
Sbjct: 126 RAHTGRPGVIAFAGGFHGRTMMGMALTGKVAPYKLGFGPFPGDVFHAPYPSALHGITSED 185

Query: 182 SLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQ 241
           +L+A++ LFKSDIEAK+VAAII EPVQGEGGF  AP + +  +R LCDEHGI++IADEVQ
Sbjct: 186 ALEAVKGLFKSDIEAKRVAAIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQ 245

Query: 242 SGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNP 301
           SG+ RTGKLFAM+HY   PDLMTMAKSLAGGMPLS V G A IMDAPAPGGLGGTYAGNP
Sbjct: 246 SGYGRTGKLFAMEHYDVLPDLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGTYAGNP 305

Query: 302 LAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDP 361
           LA+A+A AVL+++++E L  R  +LG +L+  L + + SVP IA VRG+G+M+AVEF DP
Sbjct: 306 LAIASALAVLDVMEEEQLVTRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAVEFADP 365

Query: 362 QTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDAL 419
            TG+P A   +K+QQ AL  GLLLLTCG+YGNVIRFL+PLTIPD   D A+ IL  A+
Sbjct: 366 ATGKPDAEYTKKVQQHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMDEALGILAKAI 423


Lambda     K      H
   0.319    0.134    0.388 

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: 653
Number of extensions: 18
Number of successful extensions: 1
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: 421
Length of database: 426
Length adjustment: 32
Effective length of query: 389
Effective length of database: 394
Effective search space:   153266
Effective search space used:   153266
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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