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_007727077.1 C1M55_RS03290 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::Q88RB9
         (425 letters)



>NCBI__GCF_002893965.1:WP_007727077.1
          Length = 454

 Score =  357 bits (915), Expect = e-103
 Identities = 181/421 (42%), Positives = 265/421 (62%), Gaps = 10/421 (2%)

Query: 7   SLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAA 66
           +L +RR   V  GV    P++V  A    ++DV+G  LID   GIAV + G  +P VV+A
Sbjct: 25  ALAERRKKVVGAGVASTLPVYVADADGGVIVDVDGNSLIDLGAGIAVTSVGASNPAVVSA 84

Query: 67  VQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAA 126
           VQ+Q+   +HTCF V  YE YVE+ E++ +L PGD +K+++L  +G+EAVENAVKIAR A
Sbjct: 85  VQDQVAHFTHTCFMVAPYEGYVEVAERLAELTPGDHEKRSVLFNSGAEAVENAVKIARHA 144

Query: 127 TGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRA--LFPSELHGISVDDA 184
           TGR  V+ F   YHGRT +T+ LT K +PY +G G     ++R    +P    G++VD +
Sbjct: 145 TGRDAVVVFDHAYHGRTNLTMALTSKSMPYKSGFGPFAPEVYRVPMSYPYR-EGLNVDGS 203

Query: 185 IASVER-------IFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILL 237
             + E+       + +      + AAI++EP+QGEGGF+   +  +  L A   ++G++ 
Sbjct: 204 KITGEQAAQRAITMIEKQVGAANTAAILIEPIQGEGGFIVPAEGFLPTLVAWAKENGVVF 263

Query: 238 IADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGG 297
           IADEVQ G  RTG +FA +  G+ PDL T AK IAGG PLA V G+AE +DA+ PGGLGG
Sbjct: 264 IADEVQAGFARTGAWFASDHEGIVPDLVTLAKGIAGGMPLAAVTGRAELIDAVHPGGLGG 323

Query: 298 TYAGSPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIA 357
           TY G+P+ACAAALA I+   E  L  R++ +   +   +  + K+  +IGDVRG G+M+A
Sbjct: 324 TYGGNPVACAAALASIDQMRELDLCGRARTIESTVVGRMNALAKELDVIGDVRGRGAMLA 383

Query: 358 VEVFEKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAII 417
           +E+ + G   P+A    ++ A+    G+++L+CGTYGNV+R+L PL   + LLD  L ++
Sbjct: 384 IELVKPGGQEPDADITKKIAAECLAAGVVILTCGTYGNVIRLLPPLVISEELLDDALTVL 443

Query: 418 E 418
           E
Sbjct: 444 E 444


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: 588
Number of extensions: 27
Number of successful extensions: 2
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: 454
Length adjustment: 32
Effective length of query: 393
Effective length of database: 422
Effective search space:   165846
Effective search space used:   165846
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 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