GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Desulfovibrio vulgaris Miyazaki F

Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= BRENDA::P49189
         (494 letters)



>FitnessBrowser__Miya:8501416
          Length = 1013

 Score =  233 bits (593), Expect = 3e-65
 Identities = 153/465 (32%), Positives = 230/465 (49%), Gaps = 19/465 (4%)

Query: 16  GGARVEPADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCR 75
           GG  V   D   +    +PA   VIA     G+ EV+ A++ A+ AF  W   S  +R  
Sbjct: 524 GGKDVTTDDTIASTNPAKPA--EVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAM 581

Query: 76  ILLEAARIIREREDEIATMECINNGKSIFEARLDIDISWQCLEYYAGLAASMAG-EHIQL 134
            L  AA I R R  E++  + +  GK   +A  D+      L+YYA     +     +  
Sbjct: 582 FLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGR 641

Query: 135 PGGSFGYTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAE 194
             G   +   +P G+   I  WN+PF IA   +A A+  GN ++FKPS         L E
Sbjct: 642 APGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTE 701

Query: 195 IYSEAGVPPGLFNVVQGGAAT-GQFLCQHPDVAKVSFTGSVPTGMKIMEMSAK------G 247
           I+ EAG+P G+FN V G ++  G +L +HP V+ + FTGS+  G++I E +AK       
Sbjct: 702 IFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQ 761

Query: 248 IKPVTLELGGKSPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEE 307
            K V  E+GGK+ +II  D D++ AV   L + F  QGQ C   +RV V   I D+F E 
Sbjct: 762 CKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVER 821

Query: 308 VVKQTQRIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKL 367
           +VK  Q IKIG        MGP+ +    + +L +VKVA+++G  ++   DI        
Sbjct: 822 LVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLVKRTDIPA------ 875

Query: 368 KDGYYMRPCVLTNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRD 427
            +G Y+   ++   +      +EEIFGPV++++      E L  AN T F L  GVF+R 
Sbjct: 876 -EGCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRS 934

Query: 428 IQRAHRVVAELQAGTCFINNYNVSPV--ELPFGGYKKSGFGRENG 470
            +   +   E + G  ++N  +   +    PFGG+K SG G + G
Sbjct: 935 PENLTKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVGSKTG 979


Lambda     K      H
   0.320    0.137    0.411 

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: 1129
Number of extensions: 56
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: 494
Length of database: 1013
Length adjustment: 39
Effective length of query: 455
Effective length of database: 974
Effective search space:   443170
Effective search space used:   443170
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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