GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Marinobacter adhaerens HP15

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate GFF210 HP15_209 phosphomannomutase

Query= BRENDA::Q8PGN7
         (450 letters)



>FitnessBrowser__Marino:GFF210
          Length = 452

 Score =  539 bits (1388), Expect = e-158
 Identities = 262/448 (58%), Positives = 333/448 (74%), Gaps = 13/448 (2%)

Query: 3   MTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAG 62
           M L  FKAYD+RGRVPD+LN  LA +IG A         V++G+D+RL+SP + EALS+G
Sbjct: 1   MDLSCFKAYDLRGRVPDQLNPVLAEKIGRAYVEITGAKKVIVGYDIRLSSPDIAEALSSG 60

Query: 63  LRASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDT 122
           L A+G DV DIGLCGTE+VYF T + K  GG+MVTASHNP D+NGMK+V  ++RPISSD 
Sbjct: 61  LMAAGADVFDIGLCGTEQVYFATSHYKMDGGIMVTASHNPKDHNGMKMVGPESRPISSDN 120

Query: 123 GLFAIRDTVAADTAAPGEP--TASEQSRTDK----TAYLEHLLSYVDRSTLKPLKLVVNA 176
           GL  IRD V        EP   A +Q R +     +AY++HLL Y+D  +L PL +V NA
Sbjct: 121 GLNEIRDRVL-------EPFGDAPQQGRYEPLEVMSAYVDHLLGYIDAGSLSPLTIVCNA 173

Query: 177 GNGGAGLIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGI 236
           GNGGAGL++D L  HLPFEFV+V H+PDG+FPNG+PNP+LPENR ATA AV   GA  GI
Sbjct: 174 GNGGAGLVIDELEQHLPFEFVKVHHQPDGHFPNGVPNPILPENRAATADAVIAEGAAMGI 233

Query: 237 AWDGDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGG 296
           AWDGD+DRCFFFD  GRFIEGYY+VGLLA   L K  GGKV+HDPRLTWNT++ V+ AGG
Sbjct: 234 AWDGDYDRCFFFDENGRFIEGYYIVGLLADQFLRKTGGGKVIHDPRLTWNTMDLVKAAGG 293

Query: 297 IPVLCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSL 356
             +  K+GHAFIK++MR E+AVYGGEMSAHHYFR+FAY DSGMIPWLL+AE + QSG++L
Sbjct: 294 EAIESKTGHAFIKQRMRDEDAVYGGEMSAHHYFRDFAYCDSGMIPWLLVAERLCQSGQTL 353

Query: 357 ADLVEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLR 416
           + L++AR++ +P SGEIN  + D    +A +   Y+  +  + + DG+S +F  WRFNLR
Sbjct: 354 SSLIDARIEAYPASGEINRTIDDPPKVIAAIEAKYSVGAKSVSHVDGVSIEFDDWRFNLR 413

Query: 417 SSNTEPLLRLNVETRGDAALLETRTQEI 444
            SNTEP++RLNVE+R D  L+E +T+E+
Sbjct: 414 MSNTEPVVRLNVESRADIPLMEEKTEEL 441


Lambda     K      H
   0.319    0.136    0.404 

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: 654
Number of extensions: 22
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: 450
Length of database: 452
Length adjustment: 33
Effective length of query: 417
Effective length of database: 419
Effective search space:   174723
Effective search space used:   174723
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 (21.7 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