GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Stenotrophomonas chelatiphaga DSM 21508

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_057508570.1 ABB28_RS10465 CoA transferase

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



>NCBI__GCF_001431535.1:WP_057508570.1
          Length = 398

 Score =  226 bits (575), Expect = 1e-63
 Identities = 147/404 (36%), Positives = 210/404 (51%), Gaps = 27/404 (6%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G L  +RV++   ++A P+A ++ A+ GA+VIK+E P  GD  R W     +   G+  T
Sbjct: 3   GPLHGIRVVEFGTLIAAPFAARLFAEFGAEVIKIESPEGGDPLRKW-----RQLHGD--T 55

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
              + L A RNK+SV +D    EG    R+LAA +D++IENF+ GGL   GL +D L A+
Sbjct: 56  SLWWSLQA-RNKKSVALDLKSAEGAEAARQLAASADVVIENFRPGGLEKLGLGWDVLSAM 114

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
           NP L+   I+G+GQ GPY  R G+  + + +GG+   T    GD    P +VG++L D L
Sbjct: 115 NPDLVMVRISGYGQDGPYRDRPGFGAIGEAMGGIRYTT----GDPSTPPARVGISLGDSL 170

Query: 182 TGLYST-AAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
             L+    A++A L  +   GGGQ +D++L++     + +    +   G   +R G A P
Sbjct: 171 ASLHGVMGALMALLRVKTGQGGGQVVDVSLVESVFNLMESLVPEHAMFGTVRERTGGALP 230

Query: 241 NIVPYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299
            I P   +PTADG F++  GN D  FR+     G+   ADD   ATN  RV   A L   
Sbjct: 231 GISPSNTYPTADGGFVVIAGNSDPIFRRLMRAIGRVDLADDAALATNPGRVLRNAELDAA 290

Query: 300 IRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMEL------PHLLAG 353
           I   T        +  L+ A VP G I   A + ADP  +ARG+ +E       P  L G
Sbjct: 291 ITHWTSGLHIDAVLAALDAADVPAGRIYSAADIVADPHYRARGMLLETTLPDGQPITLPG 350

Query: 354 KVPQVASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAV 397
            VP      +LS TP +     P LGEHT +VL   LG+  AA+
Sbjct: 351 IVP------KLSATPGQMHWTGPALGEHTDQVL-ATLGMTAAAI 387


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: 456
Number of extensions: 26
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: 406
Length of database: 398
Length adjustment: 31
Effective length of query: 375
Effective length of database: 367
Effective search space:   137625
Effective search space used:   137625
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