GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Collimonas arenae Ter10

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_061534093.1 CAter10_RS15355 CoA transferase

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



>NCBI__GCF_001584165.1:WP_061534093.1
          Length = 407

 Score =  216 bits (549), Expect = 1e-60
 Identities = 138/412 (33%), Positives = 215/412 (52%), Gaps = 23/412 (5%)

Query: 3   ALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTE 62
           +L  ++V++L  ++AGP+A  +L   GA+VIK+E PG+GD  R W        R  +   
Sbjct: 11  SLQGVKVIELGTLIAGPYAASLLGQFGAEVIKIESPGDGDPLRKW--------RKLHNGT 62

Query: 63  AAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAIN 122
           + ++ S +RNK+SVT++    +GQ++VR+L   +DI+IENF+ G L  +GL +D L  IN
Sbjct: 63  SLWWYSQSRNKKSVTLNLKSAQGQQIVRDLVKDADIVIENFRPGTLEGWGLGWDELSKIN 122

Query: 123 PQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILT 182
           P LI   ++G+GQ GPY  R G+  + + +GGL +L G P+      PV+VGV++ D L 
Sbjct: 123 PNLIMVRVSGYGQDGPYHARPGFAAIAESMGGLRNLAGYPD----RPPVRVGVSIGDTLA 178

Query: 183 GLYSTAAILAALAHRDHVGG-GQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
            LY     L A+ H    GG GQ ID+AL +     + +    Y   G   +R G + P 
Sbjct: 179 SLYGVIGALLAMHHLKANGGKGQFIDIALYEAVFGVMESLIPEYAEFGFVRERTGASFPG 238

Query: 242 IVPYQDFP---TADGD-FILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVL 296
           I P   +P    A+G+ +++  GN D  F++     G+   A+DP  A N  R  N  ++
Sbjct: 239 ISPSSTYPCRSDANGEHYVIIAGNGDSIFKRLMHAIGRSDLAEDPSLARNDGRAQNNDMI 298

Query: 297 IPLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVP 356
              I + T        +  LEQA VP   +   A +  DP  +AR +  +  H+L    P
Sbjct: 299 DAAIAEWTSQHDLEHVLQVLEQAEVPSSKVYTAADIHQDPHFRARDMIQQ--HVLPDGQP 356

Query: 357 QVASPI--RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
                I  +LS TP +     P LG+HT +V+   +G +   +   RE GV+
Sbjct: 357 IDLPGIVPKLSVTPGQTNWVGPELGQHT-DVVLASIGRNPEQIALLREQGVV 407


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: 446
Number of extensions: 23
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: 407
Length adjustment: 31
Effective length of query: 375
Effective length of database: 376
Effective search space:   141000
Effective search space used:   141000
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