GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Marivita geojedonensis DPG-138

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_085639734.1 MGEO_RS15340 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::Q88RB9
         (425 letters)



>NCBI__GCF_002115805.1:WP_085639734.1
          Length = 460

 Score =  490 bits (1261), Expect = e-143
 Identities = 250/422 (59%), Positives = 313/422 (74%), Gaps = 3/422 (0%)

Query: 5   NESLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVV 64
           N +L  RR  AV RGVG   P+F   A+N+ + DVEG+  IDFAGGIAVLNTGH HP V+
Sbjct: 28  NAALWARRETAVARGVGSAAPVFAARAENAELWDVEGKRYIDFAGGIAVLNTGHRHPSVI 87

Query: 65  AAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIAR 124
           AA + Q    +HT FQV+ YEPY+ L EK+N L PGDF KKTLLVTTG+EAVENAVKIAR
Sbjct: 88  AAAKAQEDLYTHTSFQVVPYEPYIALAEKLNALAPGDFAKKTLLVTTGAEAVENAVKIAR 147

Query: 125 AATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDA 184
           A TGR GVIAFT GYHGRT++TLGLTGKV PY   +G  P  IFRA FP    G++V D+
Sbjct: 148 AHTGRPGVIAFTAGYHGRTLLTLGLTGKVNPYKKDVGPFPSDIFRAPFPDTRAGLTVSDS 207

Query: 185 IASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQT 244
           + ++E +F  DA+P  +AAIILEPV GEGG+ P P E+ + LRA+CD+HGILLI+DE+Q 
Sbjct: 208 LRALETLFLTDAQPDRVAAIILEPVLGEGGYHPVPTEMWQALRAICDKHGILLISDEIQA 267

Query: 245 GAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPI 304
           G  RTGT+FA+E  GVAPDL T AKS+AGG+P+AGV G+AE MDA+ PGGLGGTY G+P+
Sbjct: 268 GFARTGTWFAIEHSGVAPDLITCAKSMAGGYPVAGVIGRAEVMDALEPGGLGGTYGGNPV 327

Query: 305 ACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYP--IIGDVRGLGSMIAVE-VF 361
           ACAAALA IE  E E LL RS A+G+ + A   +I  +     + D+RGLG+M+AVE V 
Sbjct: 328 ACAAALAAIEAIESEDLLARSTALGDTMRARFADIGARVAPFRMWDIRGLGAMLAVEFVT 387

Query: 362 EKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECF 421
           + GT TP+ A    V+A A ++GLILLSCG +GN +RI+VPLTA DA++++GLAI E   
Sbjct: 388 DFGTATPDVALTKSVIAHALKRGLILLSCGMHGNAVRIMVPLTASDAIIEEGLAIFEAAL 447

Query: 422 AE 423
           A+
Sbjct: 448 AD 449


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: 653
Number of extensions: 29
Number of successful extensions: 3
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: 460
Length adjustment: 32
Effective length of query: 393
Effective length of database: 428
Effective search space:   168204
Effective search space used:   168204
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