GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Chryseobacterium viscerum 687B-08

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_103231575.1 C1634_RS03120 phosphoglucosamine mutase

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



>NCBI__GCF_002899945.2:WP_103231575.1
          Length = 460

 Score =  294 bits (753), Expect = 4e-84
 Identities = 178/456 (39%), Positives = 260/456 (57%), Gaps = 15/456 (3%)

Query: 6   GTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPL-VVVGRDTRVSGEMLKEALISG 64
           GT G  G  N+ +TP   +K   AFGT L+    KK L +++GRD R+SG+M+   + + 
Sbjct: 12  GTIG--GKVNDNLTPLDVVKFASAFGTWLQNNKNKKDLTLIIGRDARISGQMVSSLVTAT 69

Query: 65  LLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKER 124
           L  +G +V+D+G++ TP V+      NADGG ++TASHNP ++N +KLL   G  +  E 
Sbjct: 70  LQGLGINVVDLGLSTTPTVEIMVPELNADGGIILTASHNPKQWNALKLLNEKGEFITGEN 129

Query: 125 EAIVEELFFKEDFDRAKWYEIGEVR-REDIIKPYIEAIKS--KVDVEAIKKRKPFVVVDT 181
            A V  L   EDF+ A+  ++G+   RED    +I+ I     VD EAIK +   VV+D 
Sbjct: 130 GAEVLALAESEDFNYAEVDDLGQYETREDAFDIHIKQILDLPMVDAEAIKAKNFKVVLDA 189

Query: 182 SNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVA 241
            N  G + +P LL  LGC+ + +  +P G+FP  NPEP +E+L +  E+VK   AD G+ 
Sbjct: 190 VNSTGGIAIPMLLDTLGCETVKLYCEPTGHFP-HNPEPLKEHLGDICELVKKENADLGIV 248

Query: 242 QDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHGAK 301
            D D DR   IDE G     + T   VAD +LK K  G+ V+ +++S  L D+A  H ++
Sbjct: 249 VDPDVDRLALIDEKGEMFGEEYTLVAVADYLLKHK-NGVAVSNLSSSRALRDVAHTHNSE 307

Query: 302 VMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKFS 361
              + VG++ V   + E N  IGGE NGG+I+P+   GRD  + VA  +   AK  K  S
Sbjct: 308 YFASAVGEVNVVTLMKEKNAVIGGEGNGGIIYPDLHYGRDSLVGVALFLTHLAKENKTVS 367

Query: 362 ELIDELPKYYQIKTKRHV--EGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLVR 419
           EL    P Y+  K K  +  E D  AI++K+ +    +   V   DG KI FE+ WV +R
Sbjct: 368 ELRAGYPSYFMGKKKIELTPEIDVDAILSKMEQ--EYKNEEVSVVDGVKIDFENNWVHLR 425

Query: 420 ASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKALS 455
            S TEPIIRI++EAKS+E+A +   LG +++ K  S
Sbjct: 426 KSNTEPIIRIYTEAKSQEEADK---LGDDIIAKIKS 458


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: 545
Number of extensions: 35
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: 460
Length adjustment: 33
Effective length of query: 422
Effective length of database: 427
Effective search space:   180194
Effective search space used:   180194
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 24 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