GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Escherichia coli BW25113

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 16156 b2048 phosphomannomutase (NCBI)

Query= BRENDA::Q8PGN7
         (450 letters)



>FitnessBrowser__Keio:16156
          Length = 456

 Score =  520 bits (1338), Expect = e-152
 Identities = 261/451 (57%), Positives = 325/451 (72%), Gaps = 7/451 (1%)

Query: 5   LPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLR 64
           L  FKAYDIRG++ +ELNED+A RIG A    L    +VLG DVRL S  L+ AL+ GL+
Sbjct: 4   LTCFKAYDIRGKLGEELNEDIAWRIGRAYGEFLKPKTIVLGGDVRLTSETLKLALAKGLQ 63

Query: 65  ASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGL 124
            +G DV+DIG+ GTEE+YF T +L   GG+ VTASHNPMDYNGMKLVRE ARPIS DTGL
Sbjct: 64  DAGVDVLDIGMSGTEEIYFATFHLGVDGGIEVTASHNPMDYNGMKLVREGARPISGDTGL 123

Query: 125 FAIRDTVAADTAAPGEPT--ASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182
             ++    A+   P + T     Q    + AY++HL  Y++   L PLKLV+N+GNG AG
Sbjct: 124 RDVQRLAEANDFPPVDETKRGRYQQINLRDAYVDHLFGYINVKNLTPLKLVINSGNGAAG 183

Query: 183 LIVDLLAPHL-----PFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIA 237
            +VD +         P E ++V + PDGNFPNGIPNPLLPE RD T  AV  +GAD GIA
Sbjct: 184 PVVDAIEARFKALGAPVELIKVHNTPDGNFPNGIPNPLLPECRDDTRNAVIKHGADMGIA 243

Query: 238 WDGDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGI 297
           +DGDFDRCF FD  G+FIEGYY+VGLLA+A L K PG K++HDPRL+WNTV+ V  AGG 
Sbjct: 244 FDGDFDRCFLFDEKGQFIEGYYIVGLLAEAFLEKNPGAKIIHDPRLSWNTVDVVTAAGGT 303

Query: 298 PVLCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLA 357
           PV+ K+GHAFIKE+MR E+A+YGGEMSAHHYFR+FAY DSGMIPWLL+AELV    ++L 
Sbjct: 304 PVMSKTGHAFIKERMRKEDAIYGGEMSAHHYFRDFAYCDSGMIPWLLVAELVCLKDKTLG 363

Query: 358 DLVEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRS 417
           +LV  RM  FP SGEIN K+A    ++ RV +H++  +  +D TDGIS  F  WRFNLR+
Sbjct: 364 ELVRDRMAAFPASGEINSKLAQPVEAINRVEQHFSREALAVDRTDGISMTFADWRFNLRT 423

Query: 418 SNTEPLLRLNVETRGDAALLETRTQEISNLL 448
           SNTEP++RLNVE+RGD  L+E RT+ +  LL
Sbjct: 424 SNTEPVVRLNVESRGDVPLMEARTRTLLTLL 454


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: 634
Number of extensions: 17
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: 450
Length of database: 456
Length adjustment: 33
Effective length of query: 417
Effective length of database: 423
Effective search space:   176391
Effective search space used:   176391
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