GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Marinobacter adhaerens HP15

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate GFF3996 HP15_3936 acyl-CoA dehydrogenase domain protein

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>FitnessBrowser__Marino:GFF3996
          Length = 389

 Score =  538 bits (1386), Expect = e-157
 Identities = 269/389 (69%), Positives = 311/389 (79%), Gaps = 3/389 (0%)

Query: 5   ASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGL 64
           AS  W D L  D QL E ER VRDS   F  ++L P + EA RHE+ D +IF +MGE+G+
Sbjct: 2   ASAPWNDLLGFDAQLDETERQVRDSIRSFCDEQLMPGITEANRHEKFDRSIFNQMGELGM 61

Query: 65  LGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKY 124
           LGAT+PE+YGG GLN+VCYGLIAREVER+DS YRS +SVQSSLVM PI  +G EA K++ 
Sbjct: 62  LGATLPEEYGGPGLNHVCYGLIAREVERVDSAYRSALSVQSSLVMYPIYSYGKEAMKKRI 121

Query: 125 LPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWA 184
           LPKLASGE++GCFGLTEPNHGSDP  M TRA+KVDGGY L+GSK WITNSPIADV VVWA
Sbjct: 122 LPKLASGEYVGCFGLTEPNHGSDPSGMETRAKKVDGGYLLSGSKTWITNSPIADVCVVWA 181

Query: 185 KDDAGDIRGFVLEK-GWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKG 243
           K D G + GFV+E+ G  GL  P I GK  LRAS TG I MD VFVP+EN   +V GLKG
Sbjct: 182 KLD-GKVNGFVIEREGATGLETPKIQGKFSLRASETGSIFMDEVFVPDENHL-EVEGLKG 239

Query: 244 PFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITL 303
           PF+CLN AR+GISWG+LGAAE CWH AR YTL+R+QFG+PLAANQLIQKKL DMQTEIT+
Sbjct: 240 PFSCLNKARFGISWGSLGAAEFCWHAARNYTLERKQFGKPLAANQLIQKKLVDMQTEITI 299

Query: 304 ALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLV 363
            LQ  L+LGRM D GT   +  S++KRN+CGKALDIAR+ARDM GGNGI+DE+ V RH++
Sbjct: 300 GLQAVLQLGRMMDAGTVTPDAISLLKRNNCGKALDIARVARDMHGGNGIADEYHVIRHVM 359

Query: 364 NLEVVNTYEGTHDVHALILGRAQTGIQAF 392
           NLE VNTYEGTHDVHALILGR QTGIQAF
Sbjct: 360 NLEAVNTYEGTHDVHALILGRGQTGIQAF 388


Lambda     K      H
   0.320    0.137    0.413 

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: 485
Number of extensions: 17
Number of successful extensions: 2
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: 393
Length of database: 389
Length adjustment: 31
Effective length of query: 362
Effective length of database: 358
Effective search space:   129596
Effective search space used:   129596
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: 50 (23.9 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