GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Desulfovibrio vulgaris Miyazaki F

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__Miya:8501416
          Length = 1013

 Score =  194 bits (492), Expect = 2e-53
 Identities = 131/441 (29%), Positives = 206/441 (46%), Gaps = 13/441 (2%)

Query: 23  NPAT-GDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVF 81
           NPA   +V+  + +    +VDAA+ AA  AF  W  T+P  RA  L + AD+        
Sbjct: 538 NPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAMFLHRAADIARRRMFEL 597

Query: 82  AELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGV 141
           +  +    GK    AF+D +   +D   ++A     L          G  + +   P G+
Sbjct: 598 SAWQVLEVGKQWDQAFHD-VGEGIDFLDYYAHEMLRLGTPRRMGRAPGELNHLFYQPKGI 656

Query: 142 VASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPAGVINIL 200
            A IAPWN+P  +A    A A+  GN V+ KPS I       L E+ ++   P GV N +
Sbjct: 657 AAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYV 716

Query: 201 FGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTAS------SIKRTHMELGGKAPVI 254
            GR   +GD L  HP+V M+  TGS+  G  I    A         KR   E+GGK  +I
Sbjct: 717 PGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAII 776

Query: 255 VFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDD 314
           + DDAD++  V  V    +   GQ C+A  R+     IYD  VE+L  A   +K G  +D
Sbjct: 777 IDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVERLVKAAQAIKIGPSED 836

Query: 315 ESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDAI 374
            +  +GP++  +  + + + V+ A+  G  KV+         G Y   T++ G      I
Sbjct: 837 PANYMGPVADASLQKNILEYVKVAEQEG--KVLVKRTDIPAEGCYVPLTIVEGIKPHHRI 894

Query: 375 VQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVN- 433
            Q+E+FGPV++V    N ++ +  AN +++ L   V+++      +     + G  ++N 
Sbjct: 895 AQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNR 954

Query: 434 -THFMLVSEMPHGGQKLSGYG 453
            +   +V   P GG K+SG G
Sbjct: 955 GSTGAMVERQPFGGFKMSGVG 975


Lambda     K      H
   0.317    0.134    0.397 

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: 1002
Number of extensions: 47
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 474
Length of database: 1013
Length adjustment: 39
Effective length of query: 435
Effective length of database: 974
Effective search space:   423690
Effective search space used:   423690
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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