Alignments for a candidate for pgmA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Pseudomonas fluorescens FW300-N2C3

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate AO356_12530 AO356_12530 phosphoglucomutase

Query= BRENDA::P26276
         (463 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_12530
          Length = 465

 Score =  727 bits (1877), Expect = 0.0
 Identities = 358/461 (77%), Positives = 407/461 (88%), Gaps = 2/461 (0%)

Query: 4   AKAPTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPE 63
           A AP  P SIFRAYDIRGVV +TLTAETAYWIGRAIGS+SLA+GEP V VGRDGRLSGPE
Sbjct: 6   AIAPIFPDSIFRAYDIRGVVPETLTAETAYWIGRAIGSQSLAQGEPNVCVGRDGRLSGPE 65

Query: 64  LVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAG 123
           LV+QLI+G+ D GC VSDVG+VPTP LYYAANVL GKSGVMLTGSHNP +YNGFKIV+AG
Sbjct: 66  LVEQLIKGVADSGCHVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSNYNGFKIVIAG 125

Query: 124 ETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGV 183
           +TLANEQIQAL  R++ NDL+SG GSV +VDIL RY  +I  D+ +A+ +KVVVDCGNG 
Sbjct: 126 DTLANEQIQALHTRLKTNDLSSGQGSVTKVDILERYNDEIVKDVKLARRLKVVVDCGNGA 185

Query: 184 AGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDG 243
           AGVIAPQLIEAL C VIPL+C+VDGNFPNHHPDPGK ENL+DLIAKVK  NADLGLAFDG
Sbjct: 186 AGVIAPQLIEALNCEVIPLFCDVDGNFPNHHPDPGKLENLQDLIAKVKETNADLGLAFDG 245

Query: 244 DGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVM 303
           DGDRVGVVTNTG++++PDRLLMLFA+DVV+RNP A+IIFDVKCTRRL+ LI  YGGRP+M
Sbjct: 246 DGDRVGVVTNTGSVVFPDRLLMLFARDVVARNPNAEIIFDVKCTRRLVPLIKEYGGRPLM 305

Query: 304 WKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHV 363
           WKTGHSLIKKKMK++GALLAGEMSGH+FFKERWFGFDDGIYSAARLLEILS+++  +E +
Sbjct: 306 WKTGHSLIKKKMKQSGALLAGEMSGHIFFKERWFGFDDGIYSAARLLEILSKEKSTAEEL 365

Query: 364 FSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEG-NITTLDGVRVDYPKGWGLVRA 422
           F+ FP+DISTPEINI VTE+SKF+II+AL  DAQWGEG  +TT+DGVRVDYP+GWGLVRA
Sbjct: 366 FATFPNDISTPEINIHVTEESKFSIIDAL-HDAQWGEGAELTTIDGVRVDYPQGWGLVRA 424

Query: 423 SNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463
           SNTTPVLVLRFEAD E EL+RIK VF  QLK V   L +PF
Sbjct: 425 SNTTPVLVLRFEADNEAELQRIKDVFHTQLKRVAPDLQLPF 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: 723
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources