GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas fluorescens FW300-N2E3

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate AO353_05595 AO353_05595 phosphoglucosamine mutase

Query= metacyc::MONOMER-13382
         (455 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05595
          Length = 445

 Score =  210 bits (535), Expect = 7e-59
 Identities = 151/449 (33%), Positives = 226/449 (50%), Gaps = 29/449 (6%)

Query: 3   KLFGTFGVRGIANE-KITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61
           K FGT G+RG   E  ITPEF +K+G A G   + +G  K  V+VG+DTR+SG M + AL
Sbjct: 4   KYFGTDGIRGRVGEYPITPEFMLKLGWAAGMAFRSKGACK--VLVGKDTRISGYMFESAL 61

Query: 62  ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +GL S G DV+ +G  PTPA+ + T+ FNA+ G VI+ASHNP + NGIK     G  L 
Sbjct: 62  EAGLTSAGADVMLLGPMPTPAIAYLTRTFNAEAGIVISASHNPHDDNGIKFFSGQGTKLP 121

Query: 122 KEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKV----DVEAIKKRKPF 176
            + E ++EEL         +  +IG+V R  D    YIE  KS V    +   +K     
Sbjct: 122 DDVELMIEEL-LDMPMTVVESSKIGKVSRINDASGRYIEFCKSSVPTGTNFSGLK----- 175

Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGA 236
           +V+D ++GA     P + RELG +V  ++AQPDG     N      ++ +   +V A  A
Sbjct: 176 IVIDCAHGATYKVAPSVFRELGAQVTVLSAQPDGL--NINHNCGSTHMGQLQAVVLAEHA 233

Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKG---GGLLVTTVATSNLLDD 293
           D G+A DGD DR + +D  G  + GD+   ++A   L E+G   GG++ T ++   L   
Sbjct: 234 DLGIAFDGDGDRVLMVDHTGAIVDGDELLFIIA-RDLHERGKLQGGVVGTLMSNLGLELA 292

Query: 294 IAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIF 353
           +A   G   +R  VGD  V   L E N  +GGE +G V+   H    D  +   +V+   
Sbjct: 293 LADL-GIPFVRANVGDRYVIAELLERNWLVGGENSGHVVCFSHTTTGDAIIAALQVLMSL 351

Query: 354 AKSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFED 413
            +  +  ++    L K  Q+       G  + + +   +   ER          K +   
Sbjct: 352 KRRSEGLAQSRQALRKCPQVLINVRFGGGENPVEHATVKEVSER--------VTKAMAGR 403

Query: 414 GWVLVRASGTEPIIRIFSEAKSKEKAQEY 442
           G VL+R SGTEP++R+  E + +   + Y
Sbjct: 404 GRVLLRKSGTEPLVRVMVEGEDETLVRGY 432


Lambda     K      H
   0.317    0.138    0.391 

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: 478
Number of extensions: 32
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.

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