GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Halioglobus japonicus S1-36

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_102106348.1 C0029_RS13280 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::SB2B:6938540
         (460 letters)



>NCBI__GCF_002869505.1:WP_102106348.1
          Length = 454

 Score =  499 bits (1284), Expect = e-145
 Identities = 242/440 (55%), Positives = 313/440 (71%), Gaps = 1/440 (0%)

Query: 12  LQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRK 71
           L+ +D +HHLHPFTD  D A  G RV+ RAE +YI+ A+G+K+LD M+GLWC N+GY ++
Sbjct: 10  LKQLDQSHHLHPFTDFKDYATNGGRVMSRAEHIYIYTAEGHKMLDGMSGLWCCNLGYSQR 69

Query: 72  SIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLR 131
           SI DA   QL  LP+YNNFFQC+++PAI LA  +  + P   N VFFT SGSEANDTNLR
Sbjct: 70  SIVDAVTEQLGQLPYYNNFFQCSNQPAIELAKALVDITPERFNHVFFTNSGSEANDTNLR 129

Query: 132 MVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQPYWF 191
           +V RY+  +G P KK IISRKNAYHGST+A A LGGMG MH+Q +  I  + HI+QP+WF
Sbjct: 130 LVSRYYQCQGRPEKKLIISRKNAYHGSTIAAACLGGMGPMHEQTN-GIDYVHHIEQPHWF 188

Query: 192 GEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKRIL 251
             G D  P  FG++ A+ LE KI ELGE+ VAAFIAEP QGAGGVIIPPDSYW E++RI 
Sbjct: 189 EVGPDEDPNEFGLRVARQLEEKIDELGEENVAAFIAEPVQGAGGVIIPPDSYWPEVQRIC 248

Query: 252 EKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADV 311
            + +IL I DEVI GFGRTG W+ ++T G++PDL+T AK +T+G+ P+GGV+V+D+VADV
Sbjct: 249 NERDILLIADEVICGFGRTGQWWGSETYGIEPDLMTFAKAVTNGFQPLGGVMVADKVADV 308

Query: 312 LISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLSAHPL 371
           L++  GEFAHG TYSGHP AAA  L  + IL+E  ++     +  P+ Q RLQ L+ H +
Sbjct: 309 LLAHEGEFAHGLTYSGHPAAAAAGLATLNILKEGNVIADAAANIAPHFQRRLQELADHKI 368

Query: 372 VGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMIISPPLC 431
           VG+VRG GM  A+ELV DK S     +E +  + CR    E GL++R  G+ MI++PPL 
Sbjct: 369 VGQVRGRGMFAAVELVKDKSSREPLAAESAGALFCRNTANELGLMVRQTGNAMIMAPPLI 428

Query: 432 ITRDEIDELIFKASQALSLT 451
            +  EID LI    QAL +T
Sbjct: 429 CSTSEIDSLIDMLGQALDVT 448


Lambda     K      H
   0.321    0.137    0.408 

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: 575
Number of extensions: 23
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: 460
Length of database: 454
Length adjustment: 33
Effective length of query: 427
Effective length of database: 421
Effective search space:   179767
Effective search space used:   179767
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