GapMind for catabolism of small carbon sources

 

Alignments for a candidate for man-isomerase in Pseudomonas fluorescens FW300-N1B4

Align D-mannose isomerase (EC 5.3.1.7) (characterized)
to candidate Pf1N1B4_597 N-acylglucosamine 2-epimerase (EC 5.1.3.8)

Query= reanno::WCS417:GFF4325
         (419 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_597
          Length = 419

 Score =  648 bits (1671), Expect = 0.0
 Identities = 307/402 (76%), Positives = 338/402 (84%)

Query: 9   SSWLNAPAHYVWLAAEGQRLLAFAKASRLPDGFGNLDDKGQLPADAHAETMNTARMTHSF 68
           SSWLNAPAH  WLAAEG RLLAFAKA++L +GFGNLD+KG+L A+A AETMNTARMTHSF
Sbjct: 9   SSWLNAPAHQQWLAAEGLRLLAFAKAAKLAEGFGNLDEKGRLAANAQAETMNTARMTHSF 68

Query: 69  AMAHALGLPGYAELVAHGVAALSGALRDSEHGGWFAAPHALDGNRGKAAYLHAFVALAAS 128
           AMAH  GLPG+AELV HG+ ALSG LRD+EHGGWFA P   DGN GKAAYLHAFVALAAS
Sbjct: 69  AMAHIQGLPGFAELVDHGIQALSGPLRDAEHGGWFATPEHRDGNTGKAAYLHAFVALAAS 128

Query: 129 SAVVAGAPGASTLLNDAIHIIDHFFWSEEEGVMLESFAQDWSGVEAYRGANSNMHATEAF 188
           SAVVA  PGA  LL+DAIHIID  FWSEEEG M ESF +DWS  EAYRGANSNMHATEAF
Sbjct: 129 SAVVAQRPGAQALLDDAIHIIDSHFWSEEEGAMRESFNRDWSVEEAYRGANSNMHATEAF 188

Query: 189 LALADVTGDTRWLDRALRIVERVIHTHAAGNQFMVIEHFDTHWHPLLGYNEDNPADGFRP 248
           LALADVT D RWL RA RIVERVIH HAA N ++V+EHFD  W PL  YN DNPADGFRP
Sbjct: 189 LALADVTEDNRWLIRAQRIVERVIHDHAAVNDYLVVEHFDRDWQPLRDYNYDNPADGFRP 248

Query: 249 YGITPGHGFEWARLVLHLEAARLQAGLVTPEWLVADAKRLFASACEYAWSVDGAPGIVYT 308
           YG TPGHGFEWARL+LHLEAAR+QAG++TP WL  DA++LF   C + W VDGAPGIVYT
Sbjct: 249 YGTTPGHGFEWARLLLHLEAARVQAGILTPGWLATDAQKLFDHNCRHGWDVDGAPGIVYT 308

Query: 309 LDWNHRPVVRERLHWTHAEASAAAQALLKRTGELHYETWYRRFWEFCETHFIDRLHGSWH 368
           LDW++R VVR RLHWTHAEASAAA ALLKRTG+  YE WYR FWEFC++HFIDR  GSWH
Sbjct: 309 LDWDNRAVVRHRLHWTHAEASAAASALLKRTGDEQYERWYRLFWEFCDSHFIDRCDGSWH 368

Query: 369 HELSPHNQPSSNIWGGKPDLYHAWQAVLLPALPLAPSMASAI 410
           HEL P N+PS++IW GKPDLYHAWQAVL+P LPLAPSMA A+
Sbjct: 369 HELDPLNRPSADIWAGKPDLYHAWQAVLIPRLPLAPSMAIAL 410


Lambda     K      H
   0.321    0.134    0.442 

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: 787
Number of extensions: 32
Number of successful extensions: 1
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: 419
Length of database: 419
Length adjustment: 32
Effective length of query: 387
Effective length of database: 387
Effective search space:   149769
Effective search space used:   149769
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 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