GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Cupriavidus basilensis 4G11

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate RR42_RS13475 RR42_RS13475 phosphoglucosamine mutase

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



>FitnessBrowser__Cup4G11:RR42_RS13475
          Length = 448

 Score =  216 bits (551), Expect = 9e-61
 Identities = 151/455 (33%), Positives = 236/455 (51%), Gaps = 37/455 (8%)

Query: 3   KLFGTFGVRGIANEK-ITPEFAMKIGMAFGTLL----KREGRKKPLVVVGRDTRVSGEML 57
           K FGT G+RG   E  ITP+F M++G A G +L    K+  + +P V++G+DTR+SG ML
Sbjct: 4   KYFGTDGIRGRVGEAPITPDFVMRLGYAAGMVLAHGAKQHDQARPTVLIGKDTRISGYML 63

Query: 58  KEALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNG 117
           + AL +G  S G +V+  G  PTP V + T+      G VI+ASHNP   NGIK    +G
Sbjct: 64  EAALEAGFTSAGVNVLLTGPLPTPGVAYLTRALRLSAGVVISASHNPYYDNGIKFFSADG 123

Query: 118 MGLKKEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPF 176
             L    E  +E+   +E     +  ++G  RR ED    YIE  KS    E     K  
Sbjct: 124 DKLPDAVEMAIEQA-LEEPMVCVRSDDLGRARRIEDAAGRYIEFCKSTFPYEQ-DLHKLK 181

Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGY-----FPARNPEPNEENLKEFMEIV 231
           +VVD ++GA     P++  ELG  VI++  QPDG      + A  PE       + +E V
Sbjct: 182 LVVDCAHGAAYHIAPHVFHELGADVISIGNQPDGRNINAGYGATAPE-------KLIEAV 234

Query: 232 KALGADFGVAQDGDADRAVFIDENGRFIQGDK-TFALVADAVLKEKGGGLLVTTVATSNL 290
           KA GAD G+A DGDADR   +D +GR   GD+  + +V D +   +     V T+ T+  
Sbjct: 235 KANGADLGLAFDGDADRLQVVDRDGRLFNGDELLYLIVQDRLQAGQAVEGAVGTLMTNMA 294

Query: 291 LDDIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVV 350
           ++   ++ G + +R KVGD  V   L +   T+GGE +G ++  +     DG ++  +V+
Sbjct: 295 VELAFQRQGVEFVRAKVGDRYVLEELNKRKWTLGGEGSGHLLCLDRHTTGDGIVSALQVL 354

Query: 351 EIFAKSGKKFSELIDELPKYYQ----IKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDG 406
               +SGK  S+L++ +  + Q    ++ ++  +   HA ++    +   +         
Sbjct: 355 AALRRSGKTLSQLLEGVSLFPQTLINVRVEKGFDWQSHAGLSAARAVIEPQ--------- 405

Query: 407 AKIIFEDGWVLVRASGTEPIIRIFSEAKSKEKAQE 441
              +   G VL+RASGTEP++R+  EA+  E A++
Sbjct: 406 ---LAGRGRVLIRASGTEPVVRVMVEAEKVETAEQ 437


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: 489
Number of extensions: 26
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.

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