GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Dechlorosoma suillum PS

Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Dsui_3415 Dsui_3415 FAD/FMN-dependent dehydrogenase

Query= reanno::Cup4G11:RR42_RS17300
         (497 letters)



>FitnessBrowser__PS:Dsui_3415
          Length = 486

 Score =  650 bits (1677), Expect = 0.0
 Identities = 324/464 (69%), Positives = 374/464 (80%)

Query: 16  RSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALPDNEDQVCAILRLCHS 75
           ++ALLA L +ILP   +  +PED  PYECDGL AYR +P+AVALP+ E +V AIL+LCH 
Sbjct: 15  QAALLAALGRILPPGRVYGEPEDLRPYECDGLTAYRNLPLAVALPETEAEVQAILQLCHR 74

Query: 76  LQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTAVVQPGVRNLAISEAA 135
           LQVPVVPRGA T LSGGAMP   GL+LSLAKFK+I+ VD  +RTA+VQPGVRNLA+SEAA
Sbjct: 75  LQVPVVPRGAATGLSGGAMPHHQGLLLSLAKFKKILKVDPVARTALVQPGVRNLAVSEAA 134

Query: 136 AQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRVRAVTMEGDVVEFGSE 195
           A YNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVL+VR  TM G+ V FGS 
Sbjct: 135 APYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLQVRGYTMAGEAVTFGSA 194

Query: 196 APDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFDDVAKGGNAVADVIGA 255
           A DAPG DLLA + GSEGMLAV+TEV VKL PKPQ+A+V++A FD V K GNAVA+VI A
Sbjct: 195 ALDAPGFDLLALLNGSEGMLAVITEVLVKLTPKPQVAKVVLAYFDSVTKAGNAVAEVIAA 254

Query: 256 GIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEVAEEVERMSEVLRASG 315
           GIIPAGLEMMDKPAT AVE +V+AGYDLDA A+LLCESDGTPEEV EE+  M  VL  SG
Sbjct: 255 GIIPAGLEMMDKPATHAVEPYVKAGYDLDAEAVLLCESDGTPEEVEEEIAAMRAVLEKSG 314

Query: 316 ASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKHIGTLLKRIEEMERKY 375
           A+ ++VS +E ERLRFW+GRK AFPA GRI+PDY CMDGTIPRK +  +L  I  ME+KY
Sbjct: 315 ATSLRVSANEAERLRFWAGRKAAFPAVGRITPDYLCMDGTIPRKRVAEMLTAIAAMEKKY 374

Query: 376 GLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVELGGTVTGEHGVGVEK 435
           GLRC NVFHAGDGN+HPLI++D     E  +A  FG++ILE  V LGG++TGEHGVGVEK
Sbjct: 375 GLRCANVFHAGDGNLHPLIMYDANQPGELEQATAFGAEILELSVALGGSITGEHGVGVEK 434

Query: 436 LNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEY 479
           +  MC QF+ +E   F GVK +FDPA LLNP KAIPT ARC EY
Sbjct: 435 ITQMCAQFTPEELARFEGVKQSFDPAGLLNPGKAIPTPARCREY 478


Lambda     K      H
   0.319    0.136    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: 689
Number of extensions: 15
Number of successful extensions: 1
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: 486
Length adjustment: 34
Effective length of query: 463
Effective length of database: 452
Effective search space:   209276
Effective search space used:   209276
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: 52 (24.6 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