GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-cytc in Herbaspirillum seropedicae SmR1

Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate HSERO_RS22390 HSERO_RS22390 alcohol dehydrogenase

Query= reanno::WCS417:GFF2133
         (447 letters)



>FitnessBrowser__HerbieS:HSERO_RS22390
          Length = 466

 Score =  373 bits (957), Expect = e-108
 Identities = 187/408 (45%), Positives = 255/408 (62%), Gaps = 11/408 (2%)

Query: 40  QAGATFEPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTG 99
           Q  A+ E   + RG Y+AR  DCVACH+  G APFAGGL +A+P+GAI++TNITPDK  G
Sbjct: 57  QGSASAEDQQILRGAYLARAGDCVACHTSKGGAPFAGGLALASPIGAIYSTNITPDKQHG 116

Query: 100 IGTYSLADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNI 159
           IG +S  DF R +R GV   G  +YPAMPYPSY +L+D+D++ALYA+F + + P+ Q N 
Sbjct: 117 IGDWSYEDFARLMRTGVTKAGYTVYPAMPYPSYSRLTDEDMQALYAYFSKAVPPSAQENR 176

Query: 160 PSDIPWPLNMRWPIALWNGVFAPT-ATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGL 218
            +DIPWPL+MRWP+ALW  VFAPT A Y      D    RGAY+V+G GHCGSCH+PR +
Sbjct: 177 ANDIPWPLSMRWPLALWRKVFAPTPAPYTPAAGSDQELARGAYLVEGLGHCGSCHSPRAV 236

Query: 219 AFNEKAL-DEAGAPFLAGA-LLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVV 276
              EKAL ++ G  FL+G  ++DGW  PSLR +   G+  WS+  +V+FL+TGRN +   
Sbjct: 237 TMQEKALKEDGGRLFLSGGQVVDGWSVPSLRNEHGGGIAGWSQADLVEFLRTGRNQYTAS 296

Query: 277 YGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDPQRDGAPWQYQAVAAV------QDAPG 330
           +G+M +   +S Q+M D DL A+ARYL SLP  P++  AP++Y +  A        D PG
Sbjct: 297 FGAMNDVIEDSMQYMSDADLNAMARYLLSLP--PRQQAAPYRYDSATAQAAYDGRPDGPG 354

Query: 331 AHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAY 390
           A  Y  RCA+CH  +G G  +  P LAG       ++ SAI I L G ++   +      
Sbjct: 355 ARIYLDRCAACHRSNGTGYGKAFPALAGNPVLQTSDATSAIRIILQGGRQPSTASATAGL 414

Query: 391 RMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLRGHTDPAS 438
            M  + + L D ++AEV SY+++ WGN GG   A  V K+R    P +
Sbjct: 415 VMAPYAQLLDDQQVAEVTSYIQTAWGNRGGTTTAAEVAKVRKTAVPVA 462


Lambda     K      H
   0.318    0.133    0.423 

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: 658
Number of extensions: 35
Number of successful extensions: 7
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: 447
Length of database: 466
Length adjustment: 33
Effective length of query: 414
Effective length of database: 433
Effective search space:   179262
Effective search space used:   179262
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: 51 (24.3 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