Aligments for a candidate for gabT in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for gabT in Burkholderia phytofirmans PsJN

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate BPHYT_RS30220 BPHYT_RS30220 hypothetical protein

Query= reanno::SB2B:6938540
         (460 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS30220 BPHYT_RS30220 hypothetical
           protein
          Length = 465

 Score =  346 bits (888), Expect = e-100
 Identities = 195/456 (42%), Positives = 268/456 (58%), Gaps = 11/456 (2%)

Query: 9   ISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGY 68
           I +L   D  H +HP  +      RG  V+E A G ++ DA GN+LLDA +GLWCVNVGY
Sbjct: 3   IQSLIEADRKHLIHPVINYRAHEARGVTVLESASGAFLRDAAGNELLDAFSGLWCVNVGY 62

Query: 69  GRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDT 128
           G++SI DAA AQ+Q LP+   +F    EPAI LA K+  ++P  +  V+FT  GS+A D+
Sbjct: 63  GQQSIVDAATAQMQKLPYATGYFHFGSEPAIELAQKLVEVSPASLQHVYFTLGGSDAVDS 122

Query: 129 NLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQP 188
            LR +  Y++  G PSKK II+ +  YHGS+  GA L  +   H+  DLP+P   H+  P
Sbjct: 123 ALRFITHYFNSTGRPSKKHIIALQRGYHGSSTTGAGLTALPAFHRNFDLPLPNQHHLPSP 182

Query: 189 YWFGEGRDMSPEAFGI-KTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEI 247
           Y +    D + +A  I  +  ALEAK+ ELG D VAAF  EP QG+GGVI+PP  +   +
Sbjct: 183 YAY--RNDFADDAALIAASVAALEAKVAELGADNVAAFFCEPIQGSGGVIVPPVGWLKAM 240

Query: 248 KRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDR 307
           +    K  ILF+ DEVI+GFGRTG  FA Q   ++PDL+T+AKG+T+GY PMG V++SD 
Sbjct: 241 RESCRKLGILFVADEVITGFGRTGPLFACQGENVEPDLMTVAKGLTAGYAPMGAVLMSDE 300

Query: 308 VADVLISDGGE--FAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQT 365
           +   +     E    HG TYS HPV+AA+ LE +R+  E  L+        P     L  
Sbjct: 301 IYQGIADSHAEAVVGHGHTYSAHPVSAAIGLEVLRLYHEGGLLAN-GVARAPRFARGLDA 359

Query: 366 LSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI 425
           L AHPLVG+ R  G++GA+ELVADK S   F   +        A  E+ L+ RA GD ++
Sbjct: 360 LLAHPLVGDSRHRGLLGALELVADKDSKAGFDPALKLSERIAAAAYENRLIFRAFGDNIL 419

Query: 426 -ISPPLCITRDEIDELIFKASQALSLTLEKIAARGN 460
             +P L  T  E D L+F   + L  TL+ + A+ +
Sbjct: 420 GFAPALSYTEAEFD-LMF---ERLEKTLDDVLAQAD 451


Lambda     K      H
   0.321    0.137    0.408 

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: 551
Number of extensions: 18
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: 460
Length of database: 465
Length adjustment: 33
Effective length of query: 427
Effective length of database: 432
Effective search space:   184464
Effective search space used:   184464
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the preprint on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources