GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas fluorescens FW300-N2E2

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Pf6N2E2_5269 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= BRENDA::Q88RB9
         (425 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5269
          Length = 416

 Score =  349 bits (896), Expect = e-101
 Identities = 173/414 (41%), Positives = 262/414 (63%), Gaps = 9/414 (2%)

Query: 16  VPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVS 75
           + + +  +HP+ +   KN+ V D +G+  IDF GGI VLN GH HP++V A++EQ T+++
Sbjct: 6   ISQSISIVHPVSLSHGKNAEVWDADGKRYIDFVGGIGVLNLGHCHPRIVEAIREQATRLT 65

Query: 76  HTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAGVIAF 135
           H  F    + PY+EL E++   VP D+    +L  +G+EA ENA+KI R ATGR  VIAF
Sbjct: 66  HYAFNAAPHTPYIELMERLAAFVPVDYPVSGMLTNSGAEAAENALKIVRGATGRTAVIAF 125

Query: 136 TGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKND 195
            G +HGRT+ TL L GKV PY   +G++PG ++   +PS+ +G++ ++A+ ++ER+F  +
Sbjct: 126 DGAFHGRTLATLNLNGKVAPYKQKVGVLPGPVYHLPYPSKDNGVTREEALRAMERLFSVE 185

Query: 196 AEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAM 255
            +  D+A  I+EPVQGE GFL       + LR  CD  GI+LI DE+Q+G GRTG  FA 
Sbjct: 186 IDVNDVACFIVEPVQGEAGFLAMDVLFAQALRQFCDDKGIVLIVDEIQSGFGRTGQRFAF 245

Query: 256 EQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVIEV 315
            ++G+ PDL    KSIAGG PL  V G+   +D +  GGLGGTY+G+PIACAAALA ++ 
Sbjct: 246 SRLGIEPDLVLLGKSIAGGVPLGAVVGRKALLDNLPKGGLGGTYSGNPIACAAALATLDE 305

Query: 316 FEEEKLLDRSKAVGERLTAGLREIQKK--YPIIGDVRGLGSMIAVEVFEKGTH---TPNA 370
             +  L        E + +  +  + +   P +G + G+G+M  +E+    TH   TP +
Sbjct: 306 MTDANLHAWGSQQEEAIVSRYQSWRNRGLTPYLGRLTGVGAMRGIEL----THADGTPAS 361

Query: 371 AAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEI 424
           A + Q++A ARE GL+L+  G   +++R+L PLT E  +L++GL I+E C A++
Sbjct: 362 AQLTQLLALARESGLLLMPSGKSRHIVRLLAPLTTEPNVLEEGLDILEACLAKL 415


Lambda     K      H
   0.320    0.138    0.395 

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: 18
Number of successful extensions: 2
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: 425
Length of database: 416
Length adjustment: 32
Effective length of query: 393
Effective length of database: 384
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:

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