GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas stutzeri RCH2

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate GFF3737 Psest_3806 Phosphomannomutase

Query= BRENDA::P26276
         (463 letters)



>FitnessBrowser__psRCH2:GFF3737
          Length = 857

 Score =  814 bits (2103), Expect = 0.0
 Identities = 397/463 (85%), Positives = 431/463 (93%)

Query: 1   MSTAKAPTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLS 60
           MS+AKAP LPASIFRAYDIRGVVGD+LT ETAYW+GRAIGSESLA+GEP V+VGRDGRLS
Sbjct: 395 MSSAKAPNLPASIFRAYDIRGVVGDSLTTETAYWVGRAIGSESLAKGEPNVSVGRDGRLS 454

Query: 61  GPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIV 120
           GPELV+ LIQGL+D GC VSD+GMVPTPVLYYAAN+L GKSGVMLTGSHNPPDYNGFKIV
Sbjct: 455 GPELVQHLIQGLLDSGCDVSDIGMVPTPVLYYAANILAGKSGVMLTGSHNPPDYNGFKIV 514

Query: 121 VAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCG 180
           +AG+TLANEQIQ LR+RIE NDL+SGVG VEQVD+L RYF+QIR DIAMAKPMKVVVDCG
Sbjct: 515 IAGDTLANEQIQTLRKRIENNDLSSGVGKVEQVDVLERYFQQIRSDIAMAKPMKVVVDCG 574

Query: 181 NGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLA 240
           NGVAGVIAP++IEALGC+VIPLYC+VDGNFPNHHPDPGKPENL DLIAKVK+E ADLGLA
Sbjct: 575 NGVAGVIAPRMIEALGCTVIPLYCDVDGNFPNHHPDPGKPENLVDLIAKVKSEKADLGLA 634

Query: 241 FDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGR 300
           FDGDGDRVGVVTN GT+IY DRLLMLFAKDVVSRNPGADIIFDVKCTRRL  LISGYGGR
Sbjct: 635 FDGDGDRVGVVTNAGTMIYADRLLMLFAKDVVSRNPGADIIFDVKCTRRLTPLISGYGGR 694

Query: 301 PVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDS 360
           PVMWKTGHSLIKKKMKE+GALLAGEMSGH+FFKERWFGFDDGIYSAARLLEILSQD+RD+
Sbjct: 695 PVMWKTGHSLIKKKMKESGALLAGEMSGHIFFKERWFGFDDGIYSAARLLEILSQDKRDA 754

Query: 361 EHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLV 420
           E VF+AFP DISTPEINITVTE+SKF I++ALQRDAQWGE N+ TLDGVRVDYPKGWGL+
Sbjct: 755 EQVFAAFPCDISTPEINITVTEESKFTIMDALQRDAQWGEANLITLDGVRVDYPKGWGLI 814

Query: 421 RASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463
           RASNTTPVLVLRFEAD+EEEL RI+ VFR QL  V   L +PF
Sbjct: 815 RASNTTPVLVLRFEADSEEELSRIQDVFRAQLLNVAPDLKLPF 857


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: 1147
Number of extensions: 38
Number of successful extensions: 1
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: 857
Length adjustment: 38
Effective length of query: 425
Effective length of database: 819
Effective search space:   348075
Effective search space used:   348075
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: 54 (25.4 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