GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Halomonas xinjiangensis TRM 0175

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_043526306.1 JH15_RS01440 CoA transferase

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



>NCBI__GCF_000759345.1:WP_043526306.1
          Length = 401

 Score =  450 bits (1158), Expect = e-131
 Identities = 231/405 (57%), Positives = 285/405 (70%), Gaps = 7/405 (1%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G L    VLD+SRVLAGPWAGQ+LADLGA VIK+E P  GDDTR+WGPP+L++A G    
Sbjct: 3   GPLEGRLVLDMSRVLAGPWAGQLLADLGAQVIKIEHPQRGDDTRSWGPPWLEEASG-GPQ 61

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
           EAAYYL ANR KQS+ +D   PEGQ LVR LA ++DIL+ENFKVGGL  YGLDY SL ++
Sbjct: 62  EAAYYLCANRGKQSLAVDIAHPEGQALVRALAQRADILLENFKVGGLKRYGLDYASLASL 121

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
           NP+LI CSITGFGQ GPYA RAGYDFMIQ +GGLMS+TG  EG     P+K GVA+TD++
Sbjct: 122 NPRLIGCSITGFGQEGPYAGRAGYDFMIQAMGGLMSVTGESEGL----PMKTGVAITDVM 177

Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
           TGLY+T  +LAAL  R+  G G+H+D+ALLDVQVA LANQA+N L TG  P R GNAHPN
Sbjct: 178 TGLYATIGVLAALDERERTGRGRHVDVALLDVQVATLANQALNTLVTGTDPVRHGNAHPN 237

Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301
           IVPYQ F  ADG  +LTVGND QF +FAEV G P+WADDP +A+N  RVANR  L+P+I 
Sbjct: 238 IVPYQAFACADGHLVLTVGNDTQFARFAEVLGHPEWADDPAYASNAARVANRNQLVPMIA 297

Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361
           +  + ++   W+   E  GVP GPIN L++   DPQ++ R +   L      ++PQVA+P
Sbjct: 298 KVLLSQSRDTWLAAFESRGVPAGPINTLSEALDDPQIRHREMVTRLSR-NGTEIPQVANP 356

Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           +R          APP LG+ +  VL R +GL    +   R  GV+
Sbjct: 357 LRFDGQSQTSDTAPPALGQDSDRVL-REMGLGVEDIARLRTMGVV 400


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: 569
Number of extensions: 17
Number of successful extensions: 4
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: 401
Length adjustment: 31
Effective length of query: 375
Effective length of database: 370
Effective search space:   138750
Effective search space used:   138750
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