GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas fluorescens FW300-N1B4

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate Pf1N1B4_2122 Phosphomannomutase (EC 5.4.2.8) / Phosphoglucomutase (EC 5.4.2.2)

Query= BRENDA::P26276
         (463 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2122
          Length = 465

 Score =  719 bits (1856), Expect = 0.0
 Identities = 355/459 (77%), Positives = 404/459 (88%), Gaps = 2/459 (0%)

Query: 6   APTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELV 65
           AP  P SIFRAYDIRG V + L AETAYW+GRAIGS+SLA+ EP V+VGRDGRLSGPELV
Sbjct: 8   APKFPDSIFRAYDIRGTVPEFLNAETAYWLGRAIGSQSLAQNEPNVSVGRDGRLSGPELV 67

Query: 66  KQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGET 125
           +QLI+GL D GC VSDVG+VPTP LYYAANVL GKSGVMLTGSHNP +YNGFKIV+AG+T
Sbjct: 68  EQLIKGLADSGCHVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSNYNGFKIVIAGDT 127

Query: 126 LANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAG 185
           LANEQIQAL +R++ N+L+SG GS+ QV+IL RY  +I  DI +A+ +KVVVDCGNG AG
Sbjct: 128 LANEQIQALHDRLKTNNLSSGKGSITQVEILDRYNTEIVQDIKLARRLKVVVDCGNGAAG 187

Query: 186 VIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDG 245
           VIAPQLIEAL C VIPL+CEVDGNFPNHHPDPGKPENL DLIAKVK  NADLGLAFDGDG
Sbjct: 188 VIAPQLIEALNCEVIPLFCEVDGNFPNHHPDPGKPENLVDLIAKVKETNADLGLAFDGDG 247

Query: 246 DRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWK 305
           DRVGVVTNTG+I++PDRLLMLFA+DVV+RNP A+IIFDVKCTRRLI LI  YGGRP+MWK
Sbjct: 248 DRVGVVTNTGSIVFPDRLLMLFARDVVARNPDAEIIFDVKCTRRLIPLIKEYGGRPLMWK 307

Query: 306 TGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFS 365
           TGHSLIKKKMK++GALLAGEMSGH+FFKERWFGFDDGIY+AARLLEILS+++  +E +F+
Sbjct: 308 TGHSLIKKKMKQSGALLAGEMSGHIFFKERWFGFDDGIYAAARLLEILSKEKSTAEELFA 367

Query: 366 AFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEG-NITTLDGVRVDYPKGWGLVRASN 424
            FP+DISTPEINI VTE+SKF+II+AL  DAQWGEG ++TT+DGVRVDY KGWGLVRASN
Sbjct: 368 TFPNDISTPEINIHVTEESKFSIIDAL-HDAQWGEGADLTTIDGVRVDYAKGWGLVRASN 426

Query: 425 TTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463
           TTPVLVLRFEAD E EL+RIK VF  QLK V   L +PF
Sbjct: 427 TTPVLVLRFEADDEAELQRIKDVFHVQLKRVAPDLQLPF 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: 703
Number of extensions: 19
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