GapMind for catabolism of small carbon sources

 

Aligments for a candidate for manA in Pseudomonas fluorescens FW300-N2E3

Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate AO353_05595 AO353_05595 phosphoglucosamine mutase

Query= SwissProt::Q976E4
         (455 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_05595 AO353_05595
           phosphoglucosamine mutase
          Length = 445

 Score =  157 bits (397), Expect = 7e-43
 Identities = 135/453 (29%), Positives = 202/453 (44%), Gaps = 19/453 (4%)

Query: 3   KLFGTDGVRGIVNK-ELTPELVLKLSKAIGTFFGKNS--KILVGRDVRAGGDMLVKIVEG 59
           K FGTDG+RG V +  +TPE +LKL  A G  F      K+LVG+D R  G M    +E 
Sbjct: 4   KYFGTDGIRGRVGEYPITPEFMLKLGWAAGMAFRSKGACKVLVGKDTRISGYMFESALEA 63

Query: 60  GLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRRE 119
           GL S G +V   G  PTPA+ Y  +T   + G+VI+ASHNP   NGIK     G ++  +
Sbjct: 64  GLTSAGADVMLLGPMPTPAIAYLTRTFNAEAGIVISASHNPHDDNGIKFFSGQGTKLPDD 123

Query: 120 KENEIEDLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILSHVDIEKIKKKNYKVLIDP 179
            E  IE+L   +   T+  SS   +V R +     Y+    S V          K++ID 
Sbjct: 124 VELMIEELL--DMPMTVVESSKIGKVSRINDASGRYIEFCKSSVP-TGTNFSGLKIVIDC 180

Query: 180 ANSVGALSTPLVARALGCKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTLKVDLGVA 239
           A+       P V R LG ++  ++   D L        T   + +   VV     DLG+A
Sbjct: 181 AHGATYKVAPSVFRELGAQVTVLSAQPDGLNINHNCGST--HMGQLQAVVLAEHADLGIA 238

Query: 240 HDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSSSSLVEEYLSKYN 299
            DGD DR + +D  G +  GD    +++     +  K    +V  + S+  +E  L+   
Sbjct: 239 FDGDGDRVLMVDHTGAIVDGDELLFIIARDLHERG-KLQGGVVGTLMSNLGLELALADLG 297

Query: 300 IQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLELLANENVS 359
           I      VG   +  ++ + N L G E +G  +   H    D  ++   +L  L   +  
Sbjct: 298 IPFVRANVGDRYVIAELLERNWLVGGENSGHVVCFSHTTTGDAIIAALQVLMSLKRRSEG 357

Query: 360 SAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIGKDFWFL 419
            A+    L K   V   V    G    E           ++VK ++    K +      L
Sbjct: 358 LAQSRQALRKCPQVLINVRFGGGENPVE----------HATVKEVSERVTKAMAGRGRVL 407

Query: 420 VRKSGTEPIIRIMAEAKDENVANNLVNELKKIV 452
           +RKSGTEP++R+M E +DE +      EL K+V
Sbjct: 408 LRKSGTEPLVRVMVEGEDETLVRGYAEELAKLV 440


Lambda     K      H
   0.316    0.136    0.384 

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: 427
Number of extensions: 16
Number of successful extensions: 5
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: 455
Length of database: 445
Length adjustment: 33
Effective length of query: 422
Effective length of database: 412
Effective search space:   173864
Effective search space used:   173864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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