GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh 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)



>FitnessBrowser__Miya:8501416
          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:

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