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_007736227.1 C1M55_RS16390 acetylornithine transaminase

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_002893965.1:WP_007736227.1
          Length = 399

 Score =  228 bits (580), Expect = 3e-64
 Identities = 148/422 (35%), Positives = 216/422 (51%), Gaps = 45/422 (10%)

Query: 8   LLKRRQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAV 67
           L +R  A++    G +  V   R + + + D +G++Y+DF  GIAV   GH HP V+ AV
Sbjct: 6   LQQRWSASLMNNYG-VPRVALVRGDGAVLTDADGKQYVDFLAGIAVNILGHGHPAVVEAV 64

Query: 68  QEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAAT 127
             QL  L H    + A EP +ELAE++   + G+   +     SG+EA E A K+ARA T
Sbjct: 65  TTQLSTLGHVS-NLYASEPVVELAEQLLAHL-GNVTGRAFFCNSGTEANEAAFKLARA-T 121

Query: 128 GRAGVIAFTGAYHGRTMMTLGLTGKVV------PYSAGMGLMPGGIFRALAPCELHGVSE 181
           GR  +IA  G++HGRTM  L LTG+        P  AG+  +P G   AL          
Sbjct: 122 GRKKIIAAEGSFHGRTMGALALTGQPAKRAPFEPMPAGVEFVPYGDVEAL---------- 171

Query: 182 DDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADE 241
                         A   D AA+ +EP+ GEGG  V  + ++   R +  + G LL+ DE
Sbjct: 172 ------------EQAVDSDTAAVFLEPIMGEGGVVVPPEGYLVEARRITAERGALLVLDE 219

Query: 242 VQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAG 301
           VQTG GRTG F+A + +GIVPD+ T AK +GGG PI          +   PG  G T+ G
Sbjct: 220 VQTGIGRTGWFYAHQAVGIVPDVITLAKGLGGGMPIGACIATGATAELFGPGKHGTTFGG 279

Query: 302 SPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELF 361
           +P+  AAALAVLK    E L+ R+ ++G+ + AG+ ++   H ++  VRG G ++ + L 
Sbjct: 280 NPVCAAAALAVLKTIAAEDLISRADSLGKSISAGIEDL--GHPLVDYVRGSGLLLGVVLT 337

Query: 362 EGGDTHKPAAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAEC 421
           E         ++   +   ARE G ++ +      VIR   P+ + D Q E  +A L   
Sbjct: 338 E---------DVAPAVENAAREAGYLVNAAQP--GVIRLAPPLILTDEQAETFVAALPAI 386

Query: 422 FD 423
           FD
Sbjct: 387 FD 388


Lambda     K      H
   0.319    0.137    0.393 

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: 410
Number of extensions: 21
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: 399
Length adjustment: 31
Effective length of query: 395
Effective length of database: 368
Effective search space:   145360
Effective search space used:   145360
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.

Links

Downloads

Related tools

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