GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF5428
          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:

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