GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Williamsia sterculiae CPCC 203464

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_076478048.1 BW971_RS07615 aspartate aminotransferase family protein

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



>NCBI__GCF_900156495.1:WP_076478048.1
          Length = 462

 Score =  212 bits (540), Expect = 2e-59
 Identities = 139/447 (31%), Positives = 225/447 (50%), Gaps = 31/447 (6%)

Query: 15  MDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIA 74
           +D  H  H ++  A+++  G   I  + G Y+WD  G +LLD  + L   N+G+    + 
Sbjct: 29  LDRRHVFHSWSAQAEISPMG---ITASAGSYVWDGDGRRLLDFSSMLVNTNIGHQHPRVI 85

Query: 75  DAAYAQLQTL----PFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNL 130
            A   Q   L    P Y N  +     A RL   IA   PG ++++FFT  G++AN+  +
Sbjct: 86  AAIQRQAAKLCTVAPQYANDVR---SEAARL---IAERTPGDLDKIFFTNGGADANEHAV 139

Query: 131 RMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGG--MGFMHQQGDLPIPGIVHIDQP 188
           RM R +        ++ +++R  +YHG T    +L G    + +  GD    G+VH   P
Sbjct: 140 RMARLH------TGRRKVLTRYRSYHGGTDTAINLTGDPRRWPNDHGD---SGVVHFFGP 190

Query: 189 YWF-GEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEI 247
           + +       + E    +    L+  I   G   +AA + E   G  G++IPP  Y   +
Sbjct: 191 FLYRSRFHAETEEQECARALDHLDEVIRMEGPSTIAAIVLETIPGTAGIMIPPPGYLRGV 250

Query: 248 KRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDR 307
           + + ++Y I++I DEV++GFGR+G WF+   +G+ PDL+T AKG+ SGY+P+GGV +S  
Sbjct: 251 RELCDRYGIVYIADEVMAGFGRSGTWFSVDLVGVTPDLLTFAKGVNSGYVPLGGVAISAA 310

Query: 308 VADVLISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLS 367
           +A     D   +  G TYSGHP+A A A+  I  + +E +V          +   L  L+
Sbjct: 311 IAATF--DHRPYPGGLTYSGHPLATAAAVATITAMADEDVVGNASRIGAEVIGPGLAELA 368

Query: 368 -AHPLVGEVRGMGMVGAIELVAD---KHSMVRFGSEISAGMLCREACIESGLVMRAVGDT 423
             HP VGEVRG G+  A+ELV D   +  +  +G+  +A      AC   GL+  A  + 
Sbjct: 369 DRHPSVGEVRGCGVFWALELVRDRTTREPLAPYGASSAAMNDVVAACRSGGLLPFANVNR 428

Query: 424 MIISPPLCITRDEIDELIFKASQALSL 450
           + + PP  +T +E+ E +     AL++
Sbjct: 429 IHVVPPCTVTAEEVREGLTVLDAALTV 455


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: 577
Number of extensions: 30
Number of successful extensions: 7
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: 462
Length adjustment: 33
Effective length of query: 427
Effective length of database: 429
Effective search space:   183183
Effective search space used:   183183
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