GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysN in Pseudomonas fluorescens GW456-L13

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate PfGW456L13_494 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= reanno::Putida:PP_4108
         (416 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494
           5-aminovalerate aminotransferase (EC 2.6.1.48) /
           Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase
           (EC 2.6.1.19)
          Length = 425

 Score =  338 bits (866), Expect = 2e-97
 Identities = 172/413 (41%), Positives = 257/413 (62%), Gaps = 4/413 (0%)

Query: 5   SISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRL 64
           ++ + +  +HPI     +NA V D +G+ +IDF GGI VLN GH +P V+ A+  Q  +L
Sbjct: 15  AVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKVIAAVTEQLNKL 74

Query: 65  THYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIA 124
           TH  F    + PY+ + E+++  VP  +    +L  +G+EA EN++K+AR ATG+  +IA
Sbjct: 75  THTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAGVIA 134

Query: 125 FDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184
           F G +HGRT+ TL L GKV PY   +G +PG ++   YP+   GV+ + ++ +++R+F  
Sbjct: 135 FTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKN 194

Query: 185 ELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFA 244
           +   +D+AA I EPVQGEGGF      F + LR  CD+ GIL+I DE+Q+G GRTG  FA
Sbjct: 195 DAEPKDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFA 254

Query: 245 FPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLA 304
             ++G+  DL   AKSIAGG PL  V G+ E M A+  GGLGGTY+G+PI+CAAALA + 
Sbjct: 255 MEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVME 314

Query: 305 QMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIE-FANADG-SPAPA 362
              +E+L    +   + +V+  +  +A    P IG +  +GAM  +E F N D   P  A
Sbjct: 315 VFEEEHLLDRCKAVGERLVTGLKAIQAK--YPVIGEVRALGAMIAVELFENGDSHKPNAA 372

Query: 363 QLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
            +A V+  AR +GL+L+  G   +++R+L PLT   E L++GL I+E+C +EL
Sbjct: 373 AVASVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEECFSEL 425


Lambda     K      H
   0.320    0.137    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: 496
Number of extensions: 22
Number of successful extensions: 3
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: 416
Length of database: 425
Length adjustment: 32
Effective length of query: 384
Effective length of database: 393
Effective search space:   150912
Effective search space used:   150912
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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