GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Dechlorosoma suillum PS

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate Dsui_2086 Dsui_2086 cytochrome c

Query= metacyc::MONOMER-12746
         (434 letters)



>FitnessBrowser__PS:Dsui_2086
          Length = 696

 Score =  386 bits (991), Expect = e-111
 Identities = 204/417 (48%), Positives = 269/417 (64%), Gaps = 19/417 (4%)

Query: 5   VIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGV 64
           +++ LA  G   A AA+A Q   + +GEYLAR GDCVACHTA+ GK  AGG  + TP GV
Sbjct: 28  LLSALAAAGLGRAEAADAGQ---IARGEYLARLGDCVACHTAEGGKSMAGGRELATPFGV 84

Query: 65  IYSTNITPDK-TGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAY 123
           ++STNITPDK TGIG+Y+F  FD+A+R GVA  G  LYPAMP+PSYA+++  DMQALYAY
Sbjct: 85  LFSTNITPDKETGIGNYTFAQFDRAMRKGVAADGHNLYPAMPYPSYAKMTGEDMQALYAY 144

Query: 124 FMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETP-APAAGSDPVISRGAYLVE 182
            M+G+APV + N+ + + WP + RW LS+W W F  +  TP  P AG D   +RGAYLV+
Sbjct: 145 LMQGLAPVKQANKPTAMRWPFNQRWGLSLWNWAFLDA--TPFQPDAGKDATWNRGAYLVQ 202

Query: 183 GLGHCGACHTPRALTMQEKALSASG--GSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEE 240
           GLGHCGACHTPR +  QEKA+S +G  G  FL+G   +E W A SLR       G W+ E
Sbjct: 203 GLGHCGACHTPRGIAFQEKAMSDAGSKGKHFLAGET-VESWRALSLR-------GLWTVE 254

Query: 241 QLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPK-DQPHQYD 299
               FLKTG++  +   G M++V+ HS Q++ D DL AIA YLKSLP  + +   P    
Sbjct: 255 DTALFLKTGQNRFATASGNMAEVIHHSTQHVKDEDLVAIATYLKSLPPGEHELPAPSVPR 314

Query: 300 KQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIV 359
            +VA  +     S  G   Y+  C  CHR DG+G +++FP LAGNP + + D  +L+HI 
Sbjct: 315 SEVAGKVPGNLFSSRGGLAYVQFCGDCHRQDGNGVSKIFPPLAGNPAVTAKDPATLLHIT 374

Query: 360 LKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416
           L G    +T + P  FTMP FA RL+DQE+A+++ F+RSSWGN   AV    V  +R
Sbjct: 375 LTGWKTASTAAHPRVFTMPGFA-RLNDQELAELITFVRSSWGNGGEAVTASQVKKMR 430



 Score = 31.6 bits (70), Expect = 8e-05
 Identities = 35/140 (25%), Positives = 54/140 (38%), Gaps = 33/140 (23%)

Query: 274 ADLTAIARYLKSLP-ANDPKDQ-PHQYDKQVAQALWNGDDSKPGAAVYIDNCAACHRTDG 331
           AD+ A+  Y   +  A  P+D+ P +   ++ ++L    DS  G  +Y + CA CH  +G
Sbjct: 545 ADMKAMVAYFDWMKGATKPEDKVPGRGIGKIDRSL--KPDSDNGKKIYAEQCAVCHGENG 602

Query: 332 HGYTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHSAPSTFTMPAFAWR-------- 383
            G             L+SAD   +   +    +         T+T  AF  R        
Sbjct: 603 EG-------------LKSADGKMVYPPLWGDESFNIGAGMARTYTAAAFVKRNMPIGFHG 649

Query: 384 --------LSDQEVADVVNF 395
                   LSDQE  DV  +
Sbjct: 650 KFPLGQGGLSDQEALDVAEY 669


Lambda     K      H
   0.316    0.131    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: 942
Number of extensions: 59
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 434
Length of database: 696
Length adjustment: 36
Effective length of query: 398
Effective length of database: 660
Effective search space:   262680
Effective search space used:   262680
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: 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:

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