GapMind for catabolism of small carbon sources

 

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

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate Pf1N1B4_1165 Phosphoglucosamine mutase (EC 5.4.2.10)

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1165
          Length = 445

 Score =  200 bits (509), Expect = 7e-56
 Identities = 153/459 (33%), Positives = 229/459 (49%), Gaps = 29/459 (6%)

Query: 3   KLFGTFGVRG-IANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61
           K FGT G+RG +    ITP+F LK+G A G   +  G  +  V+VG+DTR+SG M + AL
Sbjct: 4   KYFGTDGIRGRVGQYPITPDFMLKLGWAAGMAFRSMGACK--VLVGKDTRISGYMFESAL 61

Query: 62  ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +GL S G DV+ +G  PTPAI + T  F+A+ G VI+ASHNP + NGIK     G  L 
Sbjct: 62  EAGLTSAGADVMLLGPMPTPAIAYLTRTFHAEAGIVISASHNPHDDNGIKFFSGKGTKLP 121

Query: 122 KEREAIVEELFFSEDFHRAKWNEIGEL-RKEDIIKPYIEAIKNRVDVEAIKKRRPFVVVD 180
            E E ++EEL         + ++IG++ R  D    YIE  K+ V           +V+D
Sbjct: 122 DEVELMIEEL-LDTPMTVVESSKIGKVSRINDASGRYIEFCKSSVPT-GTSFTGLKIVID 179

Query: 181 TSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGV 240
            ++GA     P + RELG +VV ++AHPDG     N      +++     V A  AD G+
Sbjct: 180 CAHGATYKVAPSVFRELGAEVVVLSAHPDG--LNINENCGSTHMEPLQAAVLAEHADLGI 237

Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG---GGLLVTTIATSNL---LDDI 294
           A DGD DR   +D  G  + GD+   ++A   L+E G   GG++ T ++   L   L D+
Sbjct: 238 AFDGDGDRVQMVDHTGAVVDGDELLFIIA-RDLQERGKLQGGVVGTLMSNLGLELALADL 296

Query: 295 AKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFA 354
           A       +R  VGD  V   LLE +  +GGE +G ++        D  +   +++    
Sbjct: 297 A----IPFVRANVGDRYVISELLERDWQVGGENSGHIVCFSHTTTGDAIIAALQVLMALK 352

Query: 355 KSGKKFSELIDELPKYYQFKTKRHVEGDRKAIV-AKVAELAEKKGYKIDTTDGTKIIFDD 413
           +  +  ++    L K  Q        G    +   KV E +++          T+ +   
Sbjct: 353 RRTEGLAQSRQALRKCPQVLINVRFGGGASPLEHPKVKEASDRV---------TQAMAGR 403

Query: 414 GWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEE 452
           G VL+R SGTEP++R+  E + E + R Y E   KL+ E
Sbjct: 404 GRVLLRKSGTEPLVRVMVEGEDETQVRGYAEELAKLVTE 442


Lambda     K      H
   0.317    0.139    0.396 

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: 504
Number of extensions: 34
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: 456
Length of database: 445
Length adjustment: 33
Effective length of query: 423
Effective length of database: 412
Effective search space:   174276
Effective search space used:   174276
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.

Links

Downloads

Related tools

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