GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Desulfovibrio vulgaris Hildenborough

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= reanno::WCS417:GFF2142
         (499 letters)



>MicrobesOnline__882:208845
          Length = 1006

 Score =  200 bits (508), Expect = 2e-55
 Identities = 139/443 (31%), Positives = 204/443 (46%), Gaps = 14/443 (3%)

Query: 4   TIEHYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPI 63
           T+  YI  + V+  D           E    +  A R  + +A+AAA+ A   W DT P 
Sbjct: 511 TVPLYIGGRDVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKAALTWRDTSPA 570

Query: 64  RRARVLFEYLHLLRERKDDLARIIVAEHGKVFTDAQGEVDRGIDILEFACGIPNLLKGEH 123
            RA  L     + R+R  +L+   V E GK +  A  +V  GID LE+       L    
Sbjct: 571 DRAAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPR 630

Query: 124 SDQVSRGMDNWTMRQPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSASL 183
               + G  N    QP G+ A + P+NFP  + + M   AI  GN  I KPS        
Sbjct: 631 RMGRAPGEHNHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGY 690

Query: 184 FMAELLREAGLPKGVFNVVQGDKESV-DALIEHPDVKAVSFVGSTPIAQYIYE------T 236
            +AE+ REAGLP+GVFN   G    + D L+EHPD+  + F GS  +   I E       
Sbjct: 691 NLAEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQP 750

Query: 237 GARNGKRVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDK 296
           G R  KRV    G KN  ++  DAD+++ V  ++ +A+G  G++C A S  +++  + D+
Sbjct: 751 GQRQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDR 810

Query: 297 VIAALTERAKHLRITDGRDLKAEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPT 356
            I  L + A  + I    D    MGP+      + +S YI    + G  LL   R  +P 
Sbjct: 811 FIERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVLL--KRTDLPA 868

Query: 357 EPGLENGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSC 416
           E     G ++  T+   +  E  I +EEIFGPVLA +R   F EA+ + N   F    + 
Sbjct: 869 E-----GCYVPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAV 923

Query: 417 FTRDGNIAREFARRIEVGMVGIN 439
           F+R      +  R   VG + +N
Sbjct: 924 FSRSPEHLDKARREFRVGNLYLN 946


Lambda     K      H
   0.320    0.136    0.407 

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: 56
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: 499
Length of database: 1006
Length adjustment: 39
Effective length of query: 460
Effective length of database: 967
Effective search space:   444820
Effective search space used:   444820
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