GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Pseudomonas fluorescens GW456-L13

Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate PfGW456L13_5092 Phosphoglucosamine mutase (EC 5.4.2.10)

Query= SwissProt::Q976E4
         (455 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5092
          Length = 445

 Score =  159 bits (401), Expect = 2e-43
 Identities = 138/453 (30%), Positives = 202/453 (44%), Gaps = 19/453 (4%)

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

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

Query: 120 KENEIEDLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILSHVDIEKIKKKNYKVLIDP 179
            E+ IE+L  T    T+  SS   +V R +     Y+    S V          K++ID 
Sbjct: 124 VEHMIEELLDTPM--TVVESSKIGKVSRINDASGRYIEFCKSSVP-TGTSFTGLKIVIDC 180

Query: 180 ANSVGALSTPLVARALGCKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTLKVDLGVA 239
           A+       P V R LG ++  ++   + L        T     + A V +  K DLG+A
Sbjct: 181 AHGATYKVAPSVFRELGAEVVVLSAQPNGLNINDNCGSTHMGSLQAAVVAE--KADLGIA 238

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

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

Query: 360 SAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIGKDFWFL 419
            A+    L K   V   V    G    E            SVK  +    K +      L
Sbjct: 358 LAQSRQALRKCPQVLINVRFGGGASPLE----------HPSVKEASERVTKAMAGRGRVL 407

Query: 420 VRKSGTEPIIRIMAEAKDENVANNLVNELKKIV 452
           +RKSGTEP++R+M E +DE        EL K+V
Sbjct: 408 LRKSGTEPLVRVMVEGEDETQVRGYAEELAKLV 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: 426
Number of extensions: 19
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 (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