Alignments for a candidate for deoP in Megamonas funiformis YIT 11815

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoP in Megamonas funiformis YIT 11815

Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate WP_008538694.1 HMPREF9454_RS06625 L-fucose:H+ symporter permease

Query= TCDB::Q8XEV7
         (438 letters)



>NCBI__GCF_000245775.1:WP_008538694.1
          Length = 438

 Score =  578 bits (1490), Expect = e-169
 Identities = 280/427 (65%), Positives = 355/427 (83%), Gaps = 4/427 (0%)

Query: 6   IVQMPDGYLNKTPLFQFILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFY 65
           ++Q  DGYLNKTP+FQF+LLSCLF LWG AA+LNDILITQFKSVF+LS+FASALVQSAFY
Sbjct: 7   LIQYDDGYLNKTPIFQFVLLSCLFALWGAAASLNDILITQFKSVFTLSDFASALVQSAFY 66

Query: 66  GGYFLIAIPASLVIKKTSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGL 125
           GGYFLI+IPAS+VI+KT+YK+AI+IGL  YI GC+LFFPAS MATYTMFL AIF+IAIGL
Sbjct: 67  GGYFLISIPASVVIRKTTYKLAIMIGLIFYIGGCSLFFPASMMATYTMFLVAIFSIAIGL 126

Query: 126 SFLETAANTYSSMIGPKAYATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGM 185
            FLETA+NTYS+M+GP+ YATLRLNISQTF PIG+A+GILLGKYLVF EGESL  QMA M
Sbjct: 127 GFLETASNTYSTMLGPRKYATLRLNISQTFQPIGSASGILLGKYLVFQEGESLASQMAQM 186

Query: 186 NAEQVHNFKVLMLENTLEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRPSAL---D 242
             +Q+H F++ ML++TLEPYK MI +LV + +LFL+T++P CKV + A+++    +   +
Sbjct: 187 TPDQIHLFRLQMLQHTLEPYKIMICILVAIFILFLITKYPKCKVKEVANNQNTPKVTLGE 246

Query: 243 TLRYLASNARFRRGIVAQFLYVGMQVAVWSFTIRLALEL-GDINERDASTFMVYSFACFF 301
           TL+YL+ N  F++GIVAQFLYVGMQVAVWSFTIRLAL+L   INER A+ FMV SF CFF
Sbjct: 247 TLKYLSGNGLFKKGIVAQFLYVGMQVAVWSFTIRLALDLMPHINERMAADFMVISFVCFF 306

Query: 302 IGKFIANILMTRFNPEKVLILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGPCWATIY 361
           +GKFIAN LMT+F+  KVL+ YS+IG + + YVA  P+ +A+Y AV +S+L GPCWATIY
Sbjct: 307 VGKFIANFLMTKFSVNKVLLAYSIIGCILILYVAFIPNLTAIYAAVAISILLGPCWATIY 366

Query: 362 AGTLDTVDNEHTEMAGAVIVMAIVGAAVVPAIQGYVADMFHSLQLSFLVSMLCFVYVGVY 421
           A TL +V+ ++TE AGA+IVM+I+G A +PA+QG+V+DM  S+Q SF+V+  CF Y+G Y
Sbjct: 367 AETLKSVEKKYTETAGAIIVMSIIGGAFMPAVQGFVSDMVGSMQFSFIVNFFCFAYIGWY 426

Query: 422 FWRESKV 428
           F+ + K+
Sbjct: 427 FYYKMKL 433


Lambda     K      H
   0.329    0.139    0.412 

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: 583
Number of extensions: 22
Number of successful extensions: 3
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: 438
Length of database: 438
Length adjustment: 32
Effective length of query: 406
Effective length of database: 406
Effective search space:   164836
Effective search space used:   164836
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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
the source code
instructions for running GapMind on your computer

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