GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Phaeobacter inhibens BS107

Align Gamma aminobutyrate transaminase 1, mitochondrial; Gamma-aminobutyrate transaminase isozyme 1; LeGABA-TP1; SlGABA-T1; EC 2.6.1.96 (characterized)
to candidate GFF919 PGA1_c09350 aminotransferase class-III

Query= SwissProt::Q84P54
         (515 letters)



>lcl|FitnessBrowser__Phaeo:GFF919 PGA1_c09350 aminotransferase
           class-III
          Length = 450

 Score =  374 bits (959), Expect = e-108
 Identities = 197/438 (44%), Positives = 278/438 (63%), Gaps = 9/438 (2%)

Query: 80  TDVDPLIIEKSEGSHVYDMQGRKYIDTLAGLWCTALGGNEPRLVDAATKQLNTLPFYHSF 139
           T  + L +E+ EG +V+D  GRKYI+ LAGLWCT+LG +   ++DA T+QL+ LPF H+F
Sbjct: 12  TATEQLCLERGEGIYVFDSDGRKYIEGLAGLWCTSLGYSNTEVMDAITEQLHKLPFTHTF 71

Query: 140 WNRTTKPSLDLAKELLDMFTAKKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPNKKKFI 199
             +T +P  DLA +L  M   +  A  FF NSGS+ANDT  K++ YY NA+G+P K+K I
Sbjct: 72  GGKTHQPIQDLADKLAAMVPVED-AYIFFGNSGSDANDTHYKMLRYYFNAIGKPEKRKII 130

Query: 200 ARAKAYHGSTLISASLTGLPALHQNFDLP--APFVLHTDCPHYWRYHLPGETEEEFSTRL 257
            R + YHG T+ + SLT LPA   +FD P  A  +L  D PHY+      ETE +F  R+
Sbjct: 131 TRERGYHGVTVAAGSLTSLPANLAHFDAPLEALSILRADSPHYYTARQGNETEAQFVERI 190

Query: 258 AKNLEDLILKEGPETIAAFIAEPVMGAGGVIPPPATYFDKIQAVVKKYDILFIADEVICA 317
            +NLED I+ E P+TIAA I EP+ GA GVI PP  Y++ +QA+++KY IL  ADEVIC 
Sbjct: 191 LQNLEDQIISEDPDTIAAMIVEPITGASGVIVPPDGYYEGLQALLRKYGILIWADEVICG 250

Query: 318 FGRLGTMFGSDMYNIKPDLVTLAKALSSAYMPIGAVLVSPEVSDVIHSQSNKLGSFSHGF 377
           FGR G  FG     I PDL+T AK LSSAY PI A ++   + + +  Q+N++G F HG+
Sbjct: 251 FGRTGADFGCTTMGITPDLMTFAKQLSSAYFPISASVIPGWMYEAMVDQTNEVGVFGHGY 310

Query: 378 TYSGHPVACAVALEAIKIYKERNMVERVNRISPKFQEGLK-AFSDSPIIGEIRGLGLILA 436
           TYSGHP ACA AL+ ++IY+  N+ +    +    Q  L+  F+D P++GE+RG GLI A
Sbjct: 311 TYSGHPAACAAALKTLEIYERDNLFDHAAEVGSYLQTQLREIFTDHPLVGEVRGKGLIAA 370

Query: 437 TEFANNKSPNDHFPPEWGVGAYFGAQCQKNGMLVR-VAGDTIMMSPPFVVTPEELDELIR 495
            E  +NK+    F  +   GA     CQ NG+++R VAG+ + + PP ++T EE+D+++ 
Sbjct: 371 LELVSNKTTGASF-DKGRAGATAQRLCQDNGLILRAVAGNAVALCPPLIITREEVDDMLT 429

Query: 496 IYGKALRETEKRVEELKS 513
               A+   +   EELK+
Sbjct: 430 RLKTAI---DASYEELKA 444


Lambda     K      H
   0.318    0.135    0.402 

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: 561
Number of extensions: 16
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: 515
Length of database: 450
Length adjustment: 34
Effective length of query: 481
Effective length of database: 416
Effective search space:   200096
Effective search space used:   200096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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, 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