Alignments for a candidate for glcF in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcF in Marinobacter adhaerens HP15

Align D-lactate oxidase and glycolate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate GFF3079 HP15_3022 protein of unknown function cysteine-rich region domain protein

Query= reanno::psRCH2:GFF3770
         (405 letters)



>FitnessBrowser__Marino:GFF3079
          Length = 402

 Score =  499 bits (1284), Expect = e-146
 Identities = 246/403 (61%), Positives = 293/403 (72%), Gaps = 2/403 (0%)

Query: 1   MQTNLSEAAKKLPRAEEAESILRSCVHCGFCNATCPTYQLLGDELDGPRGRIYLMKQMFE 60
           MQTNL +        +EAESILR+CVHCGFC ATCPTYQ L DE DGPRGRIYLMK   E
Sbjct: 1   MQTNLVQQFANTKEGQEAESILRACVHCGFCTATCPTYQELNDERDGPRGRIYLMKMFLE 60

Query: 61  GGEVTESTQLHLDRCLTCRNCETTCPSGVKYHNLLDIGRDFIEQQVQRPLGERVVRGGLR 120
           G EVTE T+ HLDRCLTCR+CETTCPSGV+Y  L+DI R  +E+++ R   ++ +R  L 
Sbjct: 61  GAEVTEKTREHLDRCLTCRSCETTCPSGVQYGRLVDISRGLMEKEMPREPKDKWLRWALA 120

Query: 121 TVIPRPGLFKALLGAGNALKPLMPASLKDHLPREIRPAKPRPQVMHSRRVLILEGCVQPS 180
            VIP   LF  LL  G   +P++P  L+  +P   + A P P   HSR VL L GCVQPS
Sbjct: 121 RVIPNRQLFGVLLRLGQVFRPVLPEKLRTKVPPR-KQASPWPAASHSRIVLALAGCVQPS 179

Query: 181 LSPSTNAAAARVLDRLGISVSPAREAGCCGAVDYHLNAQDAGLDRARRNIDAWWPAIEAG 240
            +P+TNAAAARVLDRLGI++  A EAGCCGAV+YHL+  + GL+R R+NIDAWWPAIEAG
Sbjct: 180 ATPNTNAAAARVLDRLGITMVEAPEAGCCGAVNYHLSEHEKGLERMRQNIDAWWPAIEAG 239

Query: 241 AEAIVQTASGCGAFVKEYGHLLKDDPAYAAKAARVSELAKDLVEVLRSAELEKLNVRADK 300
           AEAI+ TASGCGA V++YGHLLKDDP YAAKA +VSEL  DL   L   +LEKL VR D 
Sbjct: 240 AEAIIMTASGCGAMVQDYGHLLKDDPVYAAKAQKVSELCTDLGAFLLKQDLEKLKVRQDP 299

Query: 301 -RMAFHCPCTLQHAQKLGGAVEDVLTRLGYQLTAVPDAHLCCGSAGSYSITQPEISHQLR 359
            ++AFHCPCTLQHA K  G VE VLTR G  L A  D HLCCGSAG+YS+TQPE+S +L 
Sbjct: 300 GKVAFHCPCTLQHAMKQNGVVEQVLTRAGVNLAATKDKHLCCGSAGTYSVTQPEMSQKLL 359

Query: 360 DNKLNALESGKPEVIVTANIGCQTHLDGAGRTPVKHWIEVVEE 402
            NKL AL    P+ IVTANIGCQ HL+     PV+HWIE++++
Sbjct: 360 GNKLKALTVDNPDRIVTANIGCQMHLETKSPVPVQHWIELLDQ 402


Lambda     K      H
   0.319    0.135    0.410 

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: 569
Number of extensions: 15
Number of successful extensions: 5
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: 405
Length of database: 402
Length adjustment: 31
Effective length of query: 374
Effective length of database: 371
Effective search space:   138754
Effective search space used:   138754
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources