GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Caulobacter crescentus NA1000

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate CCNA_00116 CCNA_00116 phosphoglucosamine mutase

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



>FitnessBrowser__Caulo:CCNA_00116
          Length = 448

 Score =  220 bits (560), Expect = 8e-62
 Identities = 155/441 (35%), Positives = 233/441 (52%), Gaps = 33/441 (7%)

Query: 5   FGTFGVRGIANEK-ITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALIS 63
           FGT G+RG AN+  +T E A+++G+A G L + +  ++ LVV+G+DTR+SG M++ AL++
Sbjct: 7   FGTDGIRGQANKHPMTAEVALRVGLAAGKLFRSQDERRHLVVIGKDTRLSGYMIEPALVA 66

Query: 64  GLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123
           GL SVG DV   G  PTPAV   T+   AD G +I+ASHN    NGIKL  P+G  L   
Sbjct: 67  GLTSVGLDVRLFGPLPTPAVAMMTRSMRADLGIMISASHNSFADNGIKLFGPDGYKLSDA 126

Query: 124 REAIVEELF---FKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKS----KVDVEAIKKRKP 175
           +E  +E L     +E     +  E+G V+R +D    Y+E +K+     +++  ++    
Sbjct: 127 QELGIEALMDQGLQEGLAAPR--ELGRVKRIDDAQARYVEIVKATFPRHLNLSGLR---- 180

Query: 176 FVVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALG 235
            +V+D +NGA     P  L ELG +VIT+   PDG     N E    + +   ++V+   
Sbjct: 181 -IVIDCANGAAYKVAPTALYELGAEVITLGVSPDG--TNINEECGSTHPEAMAKMVREYR 237

Query: 236 ADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKE---KGGGLLVTTVATSNL-L 291
           AD G+A DGDADR V  DE G  + GD+  A++A A  K    KGGG++ T +  SNL L
Sbjct: 238 ADIGIALDGDADRLVICDEKGVVVDGDQIMAIIAAASHKAGTLKGGGVVATVM--SNLGL 295

Query: 292 DDIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVE 351
           +      G  + RT VGD  V + + E    +GGE++G +I  +     DG +   +V+ 
Sbjct: 296 ERQLNTMGLSLERTAVGDRYVMQRMREGGFNVGGEQSGHLILSDFSTTGDGLIAALQVLA 355

Query: 352 IFAKSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIF 411
           +  ++ K  S L  +     Q+       G +      V E            DG   + 
Sbjct: 356 VMVETDKPMSALGRQFEPVPQLLENVRFVGGKPLEAAAVKEA---------IADGEAQLN 406

Query: 412 EDGWVLVRASGTEPIIRIFSE 432
             G ++VRASGTEP+IRI +E
Sbjct: 407 GAGRIVVRASGTEPLIRIMAE 427


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: 532
Number of extensions: 25
Number of successful extensions: 6
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: 448
Length adjustment: 33
Effective length of query: 422
Effective length of database: 415
Effective search space:   175130
Effective search space used:   175130
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