GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Marinobacter adhaerens HP15

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase

Query= BRENDA::Q88RB9
         (425 letters)



>FitnessBrowser__Marino:GFF3915
          Length = 422

 Score =  187 bits (476), Expect = 4e-52
 Identities = 138/407 (33%), Positives = 213/407 (52%), Gaps = 19/407 (4%)

Query: 25  PIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTK--VSHTCFQ-V 81
           P+  + AKN+ +   +G+E +DF  G   LN GH +  +  A+ E +    VS       
Sbjct: 19  PVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQGLDMFT 78

Query: 82  LAYEPYVELCEKINKLVPGDFDKKTLLV-TTGSEAVENAVKIARAATGRAGVIAFTGGYH 140
            A   ++E  +K + L P   D K      TG+  VE A+K+AR   GR+G+I+FT G+H
Sbjct: 79  TAKHDFMESYKK-HILDPRGLDYKMQFTGPTGTNCVEAALKLARKVKGRSGIISFTNGFH 137

Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKNDAEPRD 200
           G TM  +  TG    +  G+G   G +    +   L G  VD  +A ++++  + +   +
Sbjct: 138 GVTMGAVATTGNK-HHRGGVGTPLGNVDFMFYDGYL-GDDVD-TLAIMDKLLSDGSSGFE 194

Query: 201 I-AAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMG 259
           + AA+I+E VQGEGG      E +K L  LC +H ILLI D++Q G GRTG FF+ E  G
Sbjct: 195 LPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEFFSFEFAG 254

Query: 260 VAPDLTTFAKSIAG-GFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVIE-VFE 317
           + PD+ T +KS++G G P+A V  K E +D   PG   GT+ G+ +A   A A +E  ++
Sbjct: 255 IKPDIVTVSKSLSGYGLPMALVLFKPE-LDVWDPGEHNGTFRGNNMAFITARAAVENYWK 313

Query: 318 EEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVFEKGTHTPNAAAVGQVV 377
           ++   +  KA  E L   L+ I  KYP    ++G G M       +G    +A   G + 
Sbjct: 314 DDAFANEVKAKTEVLGDALQSICDKYPGQFKMKGRGLM-------RGIEAKHADITGPIT 366

Query: 378 AKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEI 424
            +A E GLI+ + G    V++ L+PLT  +  L KG A++ +   EI
Sbjct: 367 KRAFEHGLIIETSGPNDEVIKCLMPLTTSEEDLKKGAALLAKSVDEI 413


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: 466
Number of extensions: 25
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: 425
Length of database: 422
Length adjustment: 32
Effective length of query: 393
Effective length of database: 390
Effective search space:   153270
Effective search space used:   153270
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