GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Rhodococcus qingshengii djl-6-2

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_007731008.1 C1M55_RS18665 diaminobutyrate--2-oxoglutarate transaminase

Query= reanno::pseudo3_N2E3:AO353_11510
         (425 letters)



>NCBI__GCF_002893965.1:WP_007731008.1
          Length = 420

 Score =  179 bits (454), Expect = 1e-49
 Identities = 141/435 (32%), Positives = 218/435 (50%), Gaps = 37/435 (8%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLH 60
           M+   AS+ +  E+ V R   +  P     A  S + D  GR+++DF  G   LN GH +
Sbjct: 1   MNINEASIFETLESEV-RSYCRDWPAVFTSASGSWIRDENGRDYLDFFAGAGALNYGHNN 59

Query: 61  PKVIAAVTEQL--NKLTHTC-FQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVE 117
           P + +A+ + +  + +TH      +A   ++E  ++   +  G   K      TGS  VE
Sbjct: 60  PVLKSALVDYIMSDGITHGLDMSTVAKREFLETFQRNILEPRGLDYKVQFPGPTGSNTVE 119

Query: 118 NSIKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELH 177
            ++K+AR  TGR+ VI FT A+HG T+  L +TG  +   AG G+         + N   
Sbjct: 120 AALKLARKVTGRSAVINFTNAFHGMTLGALSVTGNSMK-RAGAGVPLVHTTPMPFDNYFD 178

Query: 178 GVS---------IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRA 228
           GV+         +DDS + I R           AA+I+E VQGEGG  VA  E+++ L  
Sbjct: 179 GVTEDFQWFSRVLDDSGSGINRP----------AAVIVETVQGEGGVNVARPEWLRALAT 228

Query: 229 LCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAG-GFPLAGVCGKAEYM 287
           LC   GILLI D+VQ G GRTG FF+ E+ G+  D+ T +KSI+G G P+A    K E +
Sbjct: 229 LCSDRGILLIVDDVQMGCGRTGPFFSFEEAGIVPDIVTLSKSISGYGMPMALTLFKRE-L 287

Query: 288 DAIAPGGLGGTYAG-SPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVI 346
           D   PG   GT+ G +P    + +A+   + ++ L       G R+      +  ++P  
Sbjct: 288 DVWGPGEHNGTFRGNNPAFVTSKVALDHYWSDDALTKTTLKKGARISECFANLSDQFP-- 345

Query: 347 GEVRALG-AMIAVELFENGDSHKPNAAAVAKVVAKARDKGLILLSCGTYGNVLRVLVPLT 405
           GEV   G  ++   +FE     +P  A   KV   A D+GL+  + G    V+++L  LT
Sbjct: 346 GEVSHRGRGLVQGLVFE-----QPERA--GKVCQLAFDEGLLAETSGPSDQVVKLLPALT 398

Query: 406 APDEQLDKGLAIMEE 420
             D++L+ GL+I+ E
Sbjct: 399 ITDDELEHGLSILAE 413


Lambda     K      H
   0.320    0.137    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: 428
Number of extensions: 18
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: 420
Length adjustment: 32
Effective length of query: 393
Effective length of database: 388
Effective search space:   152484
Effective search space used:   152484
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 24 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