GapMind for catabolism of small carbon sources

 

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

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate H281DRAFT_00095 H281DRAFT_00095 beta-alanine--pyruvate transaminase

Query= BRENDA::Q88RB9
         (425 letters)



>FitnessBrowser__Burk376:H281DRAFT_00095
          Length = 443

 Score =  171 bits (432), Expect = 5e-47
 Identities = 142/430 (33%), Positives = 208/430 (48%), Gaps = 48/430 (11%)

Query: 25  PIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAY 84
           P  + +AK       +GR ++D   G+  +N GH   ++VAAVQ Q  ++       + +
Sbjct: 29  PRLLASAKGMYYTSHDGRRILDGTAGLWCVNAGHCRDEIVAAVQAQAAEMDFAPTFQMGH 88

Query: 85  EPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARA---ATGRAGVIAFTG---G 138
               E   KI +  PGD  K    V +GSEAV+ A+KIA A   + G      F G   G
Sbjct: 89  PKAFEAATKIARHTPGDL-KHIFFVNSGSEAVDTALKIALAYHRSRGEGQRTRFIGRERG 147

Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSE---LHGISVDDAIAS-------- 187
           YHG     + + G      A  G        AL PS     H +++ +A  S        
Sbjct: 148 YHGVGFGGISVGGIAPNRKAFSG--------ALLPSIDHLPHTLNIKEAAYSKGQPAWGA 199

Query: 188 -----VERIFK-NDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADE 241
                +ERI   +DA    +AA+I+EPV G  G L  P+  ++RLR +CD+HGILLI DE
Sbjct: 200 HLADELERIVALHDAST--VAAVIVEPVAGSTGVLIPPQGYLQRLREICDKHGILLIFDE 257

Query: 242 VQTGAGRTGTFFAMEQMGVAPDLTTFAKSI-AGGFPLAGVCGKAEYMDAI---APGGL-- 295
           V TG GR G  FA +  GV PDL T AK       P+  V    +  D+I   APGG+  
Sbjct: 258 VITGWGRLGAPFAAQYFGVTPDLLTMAKGTNNAAAPMGAVAASGQIHDSIVNGAPGGIEL 317

Query: 296 --GGTYAGSPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLG 353
             G TY+G PIA AAA A I+++E E+L D++  +       + +++ +  +I DVR LG
Sbjct: 318 FHGYTYSGHPIAAAAACATIDLYEREQLFDQAARMAPLFERAIHKLRGERHVI-DVRNLG 376

Query: 354 SMIAVEVFEKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKG 413
            +  VE+  +    P   A   V  +  +KG++       G++L    PL  E+A +D+ 
Sbjct: 377 LVGGVELAPR-DGAPGTRAY-DVFVRCFQKGVLTRYT---GDILAFSPPLIIEEAQIDEI 431

Query: 414 LAIIEECFAE 423
            A + E   E
Sbjct: 432 FATVAEVLRE 441


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: 514
Number of extensions: 28
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: 425
Length of database: 443
Length adjustment: 32
Effective length of query: 393
Effective length of database: 411
Effective search space:   161523
Effective search space used:   161523
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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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