GapMind for catabolism of small carbon sources

 

Aligments for a candidate for DVU3033 in Desulfovibrio vulgaris Hildenborough

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 207247 DVU1782 iron-sulfur cluster-binding protein

Query= uniprot:Q726S3
         (717 letters)



>lcl|MicrobesOnline__882:207247 DVU1782 iron-sulfur cluster-binding
           protein
          Length = 475

 Score =  287 bits (735), Expect = 7e-82
 Identities = 165/420 (39%), Positives = 231/420 (55%), Gaps = 10/420 (2%)

Query: 4   SKTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAA 62
           S T  +++  +  +L +  LR          RA R N F D +E   +    +A K  A 
Sbjct: 3   SSTSIDFKGNVTGALADRQLRANFRSALDGLRAKRLNVFSDAEELDRMRVQGEANKRRAL 62

Query: 63  KNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLN 122
             +  L  Q +      G+ VH A T  EAN I+  I R ++    +K KSM +EE HLN
Sbjct: 63  AQLPALLEQLEHRCTANGIIVHWAETTDEANRIVLDIMRSHDATTLVKGKSMVSEEMHLN 122

Query: 123 HRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQR 182
             LE   +E +ETDLGE+IIQ+ HE PSH+++PA+H +R QVA +F E   +    ++++
Sbjct: 123 AYLERHGIEALETDLGEFIIQLNHEPPSHIIVPAVHKNRQQVARIFHEKLGEPYVDEVEK 182

Query: 183 LVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDK 242
           L  +ARR LR  F TA +G+SG NFA+AETGT+ LV NEGN R+ TT+P VH+AL GL+K
Sbjct: 183 LNAIARRTLREKFRTAQVGLSGVNFAIAETGTLLLVENEGNGRMCTTVPPVHIALMGLEK 242

Query: 243 LVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALA 302
           +V  L D    L++L  +ATGQ +T+YV  I    +     DG +E+H+V LDNGR  + 
Sbjct: 243 VVERLEDVPPLLRLLTGSATGQLVTTYVNCITSPRK-PGEKDGPREVHLVILDNGRSRML 301

Query: 303 EDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQN 362
            DP  S+ L+C+RCG C N CPVY  +GGH    +Y G IG ILT    G  +   L   
Sbjct: 302 ADPQLSRTLQCIRCGTCLNHCPVYVRIGGHAYDSVYPGPIGKILTPQIDGLARKGVLATA 361

Query: 363 CINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFAKW 422
              C +C+ +C   I +P L++ +R    E    P E  + G   K      TL   A W
Sbjct: 362 SSLCNACEEVCPVRIPIPALLRRLR---RESYAPPGEGVVKGAGSK-----RTLFEKAVW 413


Lambda     K      H
   0.321    0.135    0.402 

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: 751
Number of extensions: 27
Number of successful extensions: 3
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: 717
Length of database: 475
Length adjustment: 36
Effective length of query: 681
Effective length of database: 439
Effective search space:   298959
Effective search space used:   298959
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 (21.9 bits)
S2: 53 (25.0 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