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_076948621.1 C1M55_RS28045 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::Q88RB9
         (425 letters)



>NCBI__GCF_002893965.1:WP_076948621.1
          Length = 457

 Score =  379 bits (973), Expect = e-109
 Identities = 197/426 (46%), Positives = 264/426 (61%), Gaps = 7/426 (1%)

Query: 5   NESLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVV 64
           + +L +RR AA+P G+     I+V  A    V+DV+    IDF  GIAV   G+  P+VV
Sbjct: 32  SRALAKRRSAALPAGLTSGSSIYVAAAGGGVVVDVDDNSFIDFGSGIAVTTVGNSAPRVV 91

Query: 65  AAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIAR 124
                QL + +HTCF    YE Y+E+CE +N+L PGD +K+T L  TGSEA+ENAVK AR
Sbjct: 92  ERTTRQLGQFTHTCFLANPYEGYLEVCEALNRLTPGDHEKRTALFNTGSEALENAVKYAR 151

Query: 125 AATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRA------LFPSELHG 178
           AATGR  V+ F   +HGRT+MT+ +T K  PY A  G     ++R        +PS    
Sbjct: 152 AATGRPAVVVFDHAFHGRTLMTMTMTAKNQPYKATFGPFAPEVYRVPMAYPYRWPSGPEN 211

Query: 179 ISVDDAIASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLI 238
            + D+A A              +AA+++EP+QGEGGF+      +KR+   C + GIL++
Sbjct: 212 -AADEAFAQFRLAIDTQIGAESVAAVVVEPIQGEGGFIVPAPGFLKRISEFCRERGILVV 270

Query: 239 ADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGT 298
           ADEVQTG  RTG++FA E     PD+ T AK +AGG PLA V G+A+ MDA  PGG+GGT
Sbjct: 271 ADEVQTGIARTGSWFASESEDFVPDIITTAKGLAGGMPLAAVTGRADVMDAAHPGGIGGT 330

Query: 299 YAGSPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAV 358
           Y+G+P+AC AALAV E  E E LLDR+K +G+ LT GL EI     IIGD+RG G+MIA+
Sbjct: 331 YSGNPVACEAALAVFETIEMEGLLDRAKDIGDILTTGLSEIASDTDIIGDIRGRGAMIAI 390

Query: 359 EVFEKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIE 418
           E+       PN  AV Q+V+ A   GL+LL+ GTYGNV+R L PL+  D LL +GL I+ 
Sbjct: 391 ELVHDEDKAPNREAVAQIVSYAHAHGLLLLTAGTYGNVVRFLPPLSISDELLTEGLGILR 450

Query: 419 ECFAEI 424
           +  A +
Sbjct: 451 DAVAAV 456


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: 615
Number of extensions: 28
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: 457
Length adjustment: 32
Effective length of query: 393
Effective length of database: 425
Effective search space:   167025
Effective search space used:   167025
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