GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Desulfovibrio vulgaris Miyazaki F

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__Miya:8501416
          Length = 1013

 Score =  221 bits (562), Expect = 1e-61
 Identities = 157/477 (32%), Positives = 231/477 (48%), Gaps = 46/477 (9%)

Query: 23  FINGEYTDAVSGETFECLSPVD-GRFLAKVASCDLADANRAVENARATFNSGVWSQLAPA 81
           FI G+  D  + +T    +P      +A+V      + + A+E A+  F +  W   +PA
Sbjct: 522 FIGGK--DVTTDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPA--WRDTSPA 577

Query: 82  KRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141
            R   L R AD+ R+ + EL+  + L++GK              QA H   E ID + D 
Sbjct: 578 DRAMFLHRAADIARRRMFELSAWQVLEVGKQWD-----------QAFHDVGEGIDFL-DY 625

Query: 142 VAPTPHDQLGLVTR---------------EPVGVVGAIVPWNFPLLMACWKLGPALATGN 186
            A   H+ L L T                +P G+   I PWNFP  +A      A+ TGN
Sbjct: 626 YA---HEMLRLGTPRRMGRAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGN 682

Query: 187 SVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGST 246
            V+ KPS  +      + ++  EAG+P GV N +PG    +G  L  H  V  + FTGS 
Sbjct: 683 PVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSM 742

Query: 247 KIA-----KQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEV 301
           ++      K   V  G+   KR+  E GGK+  I+  DA   +A  +   SA  F QG+ 
Sbjct: 743 EVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGF-QGQK 801

Query: 302 CTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGH 361
           C+A SR++V   I D+F+  +V+A +  K G   DP   +G + D      +L Y++   
Sbjct: 802 CSACSRVIVLDPIYDRFVERLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAE 861

Query: 362 KDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAI 421
           ++G  L+   KRT     G YV  TI +G+    RIAQEEIFGPVL+V+     +EA+AI
Sbjct: 862 QEGKVLV---KRTDIPAEGCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAI 918

Query: 422 ANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMT--APFGGFKQSGNG 476
           AN T + L  G+++       K  R  R G++++N+   G M    PFGGFK SG G
Sbjct: 919 ANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVG 975


Lambda     K      H
   0.316    0.132    0.390 

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: 1072
Number of extensions: 44
Number of successful extensions: 6
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: 497
Length of database: 1013
Length adjustment: 39
Effective length of query: 458
Effective length of database: 974
Effective search space:   446092
Effective search space used:   446092
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 (21.6 bits)
S2: 55 (25.8 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