GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Desulfovibrio vulgaris Miyazaki F

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= BRENDA::Q8BH00
         (487 letters)



>lcl|FitnessBrowser__Miya:8501416 DvMF_2146
           delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
          Length = 1013

 Score =  240 bits (613), Expect = 1e-67
 Identities = 156/482 (32%), Positives = 248/482 (51%), Gaps = 19/482 (3%)

Query: 13  FIGGKFLPCNSYIDSYDPST-GEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQERSL 71
           FIGGK +  +  I S +P+   EV  +V   GK E++AA+EAA++AFPAW   SP +R++
Sbjct: 522 FIGGKDVTTDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAM 581

Query: 72  VLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSECTQM 131
            L+R AD+  + + EL+  +  + GK    A   D+   +    ++A   L   +     
Sbjct: 582 FLHRAADIARRRMFELSAWQVLEVGKQWDQA-FHDVGEGIDFLDYYAHEMLRLGTPRRMG 640

Query: 132 SHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFC 191
              G +++    P GIA +I+PWN P  +     A AI  GN VI KPS + S   +   
Sbjct: 641 RAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLT 700

Query: 192 KLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAP------ 245
           ++  +AG+P GV N V G    +G+ LV HP+V +I FTGS     RI + +A       
Sbjct: 701 EIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQM 760

Query: 246 HCKKLSLELGGKNPAIIFEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLK 305
            CK++  E+GGKN  II +DA+L+E +   + S+F  QG+ C   SR+ V   IY  F++
Sbjct: 761 QCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVE 820

Query: 306 RFVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPL 365
           R V+A +  K+G   DP+  MG +   +  + +  YV  A+ EG  +     V +  +P 
Sbjct: 821 RLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVL-----VKRTDIPA 875

Query: 366 RNQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWS 425
               G ++  T++  IK   R   EEIFGPV  V+   + +E +  AN  R+ L   V+S
Sbjct: 876 E---GCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFS 932

Query: 426 KDVGRIHRVAKKLQSGLVWTNCWLIREL--NLPFGGMKSSGIG-REGAKDSYDFFTEIKT 482
           +    + +  ++ + G ++ N      +    PFGG K SG+G + G  D    F + + 
Sbjct: 933 RSPENLTKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVGSKTGGPDYLLQFMDPRC 992

Query: 483 IT 484
           +T
Sbjct: 993 VT 994


Lambda     K      H
   0.319    0.134    0.404 

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: 1042
Number of extensions: 51
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: 487
Length of database: 1013
Length adjustment: 39
Effective length of query: 448
Effective length of database: 974
Effective search space:   436352
Effective search space used:   436352
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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