GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Pseudomonas simiae WCS417

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate GFF5428 PS417_27785 phosphoglucomutase

Query= BRENDA::P26276
         (463 letters)



>lcl|FitnessBrowser__WCS417:GFF5428 PS417_27785 phosphoglucomutase
          Length = 465

 Score =  728 bits (1879), Expect = 0.0
 Identities = 365/466 (78%), Positives = 404/466 (86%), Gaps = 4/466 (0%)

Query: 1   MSTAK--APTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGR 58
           MSTA    PT P SIFRAYDIRGVV  TLTAETAYWIGRAIGS+SLA+ EP V+VGRDGR
Sbjct: 1   MSTAARVVPTFPDSIFRAYDIRGVVPKTLTAETAYWIGRAIGSQSLAQDEPNVSVGRDGR 60

Query: 59  LSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFK 118
           LSGPELV+QLIQGL D GC VSDVG+VPTP LYYAANVL GKSGVMLTGSHNP DYNGFK
Sbjct: 61  LSGPELVEQLIQGLADSGCHVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSDYNGFK 120

Query: 119 IVVAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVD 178
           IV+AG+TLANEQIQAL +R++ NDL SG G+V +VDIL RY  +I  D+ +A+ +KVVVD
Sbjct: 121 IVIAGDTLANEQIQALHDRLKNNDLTSGKGTVTKVDILQRYSDEITRDVKLARRLKVVVD 180

Query: 179 CGNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLG 238
           CGNG AGVIAPQL+EAL C VIPL+CEVDGNFPNHHPDPGKPENL DLIAKVK   AD+G
Sbjct: 181 CGNGAAGVIAPQLLEALNCEVIPLFCEVDGNFPNHHPDPGKPENLVDLIAKVKETGADVG 240

Query: 239 LAFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYG 298
           LAFDGDGDRVGVVT TG I++PDRLLMLFA+DVV+RN  A+IIFDVKCTRRL  LI  YG
Sbjct: 241 LAFDGDGDRVGVVTETGEIVFPDRLLMLFARDVVARNANAEIIFDVKCTRRLTPLIKEYG 300

Query: 299 GRPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQR 358
           GRP+MWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILS+++ 
Sbjct: 301 GRPLMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSKEKS 360

Query: 359 DSEHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEG-NITTLDGVRVDYPKGW 417
            +E +F  FP+DISTPEINI VTE+SKF+II+AL  DAQWGEG N+TT+DGVRVDY KGW
Sbjct: 361 TAEELFQTFPNDISTPEINIHVTEESKFSIIDAL-HDAQWGEGANLTTIDGVRVDYAKGW 419

Query: 418 GLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463
           GLVRASNTTPVLVLRFEADTE EL+RIK VF  QLK V   L +PF
Sbjct: 420 GLVRASNTTPVLVLRFEADTEAELQRIKDVFHAQLKRVAPDLQLPF 465


Lambda     K      H
   0.319    0.138    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: 716
Number of extensions: 18
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: 463
Length of database: 465
Length adjustment: 33
Effective length of query: 430
Effective length of database: 432
Effective search space:   185760
Effective search space used:   185760
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 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