GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Haloterrigena daqingensis JX313

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_076582976.1 BB347_RS13070 CoA transferase

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>NCBI__GCF_001971705.1:WP_076582976.1
          Length = 404

 Score =  276 bits (707), Expect = 6e-79
 Identities = 151/403 (37%), Positives = 228/403 (56%), Gaps = 14/403 (3%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  + VLDLS  + G +   +LA+ GA+V+K+E+PG GD  R  GPPF++        E+
Sbjct: 8   LEGVTVLDLSTFVTGGFCSAMLANQGAEVLKIEQPGYGDAIRHSGPPFIEG-------ES 60

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
            YY + N  K+S+ +D   P  +  + EL  ++DI I+NF+ G      +DYD++   N 
Sbjct: 61  PYYWTVNYGKKSLELDLKNPRAKEALYELVEETDIFIQNFRPGTAERLEVDYDTIAQHNE 120

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
            +IY +I+ FGQTGP+ +RAGYD +IQG+GG+M +T    G+EG  PVK G+ +TD++T 
Sbjct: 121 DVIYLAISAFGQTGPWRERAGYDLLIQGMGGIMDVT----GEEGRQPVKTGLPMTDLITS 176

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243
           ++++   + AL  R+  G G++ID+ +L+  +  L  QA   +  GN  +R+G   P + 
Sbjct: 177 MWASFGAMTALYRRERTGDGEYIDLGMLESTLPWLTKQA-GQVFAGNETRRMGTKDPVLA 235

Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303
           PYQ F T DG   + + N+  + +  E   +P   +D RF TN  RV +   L   I   
Sbjct: 236 PYQTFETKDGFLNVCILNEKLWGELCEALERPDLPEDDRFETNADRVDHLDALEAEIEAT 295

Query: 304 TVFKTTAEWVTQL-EQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPI 362
              KTT EW+  + E AGVP GP+ D+ +   +PQ++ARG   EL H   G VP +  P+
Sbjct: 296 LGTKTTDEWIEIIAEDAGVPAGPVYDVEEALTNPQIEARGTITELEHPELGTVPVIEHPL 355

Query: 363 RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGV 405
           +       +  APPLLGEH  +V  R LG  EA +    E GV
Sbjct: 356 KFDRAETGFDRAPPLLGEHNRDVF-RDLGYTEAELDELAEEGV 397


Lambda     K      H
   0.319    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: 441
Number of extensions: 25
Number of successful extensions: 5
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: 406
Length of database: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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 (21.7 bits)
S2: 50 (23.9 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