GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Paraburkholderia bryophila 376MFSha3.1

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate H281DRAFT_04057 H281DRAFT_04057 acetylornithine aminotransferase apoenzyme

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Burk376:H281DRAFT_04057
          Length = 394

 Score =  174 bits (440), Expect = 6e-48
 Identities = 131/398 (32%), Positives = 196/398 (49%), Gaps = 45/398 (11%)

Query: 35  VWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMN 94
           ++D  G+ YLDF  G AV   GH    ++ A+  Q K L +        EP  +L  ++ 
Sbjct: 30  LYDNNGKRYLDFIQGWAVNCLGHCDEGMIEALNQQAKLLFNPS-PAFYNEPMAKLAALLT 88

Query: 95  QKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGT-----IAFSGAYHGRTHYTLALT 149
           Q    D   K     +G+EA E A+K+AR   K+        I F  ++HGRT  T++ +
Sbjct: 89  QHSCFD---KVFFANSGAEANEGAIKLARKWGKKFKDGAFEIITFDHSFHGRTLATMSAS 145

Query: 150 GKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDA--IASIHRIFKNDAAPEDIAAIVIEP 207
           GK           PG  +  +Y   + G  + D   IAS+ ++           A+++EP
Sbjct: 146 GK-----------PG--WDTIYAPQVPGFPKADLNDIASVEKLINAKTV-----AVMLEP 187

Query: 208 VQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFA 267
           +QGEGG   ++  FMQ+LR L  +H ++LI DEVQSG GR GTLFA E  GV PD+ T  
Sbjct: 188 IQGEGGVIPATREFMQQLRELTRKHNVLLIVDEVQSGCGRAGTLFAYELSGVEPDIMTLG 247

Query: 268 KSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQKANDL 327
           K I GG PLA +  +AEV      G  GGTY GNP+       V+        L+     
Sbjct: 248 KGIGGGVPLAALLAKAEVA-VFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGVRAR 306

Query: 328 GQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARD---KG 384
           G+ L+  LL ++E+    G+ RG G + A+ L +D         +  +IV +ARD    G
Sbjct: 307 GEYLRAKLLELSEERGFKGE-RGEGLLRALLLGKD---------IGNQIVEKARDMQPDG 356

Query: 385 LILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422
           L+L +  P  N+LR +  L + + +I Q + ++    D
Sbjct: 357 LLLNAARP--NLLRFMPALNVTNEEIDQMMAMLRSILD 392


Lambda     K      H
   0.320    0.137    0.401 

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: 427
Number of extensions: 28
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: 426
Length of database: 394
Length adjustment: 31
Effective length of query: 395
Effective length of database: 363
Effective search space:   143385
Effective search space used:   143385
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