GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Psychromonas ossibalaenae JAMM 0738

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_019612989.1 G327_RS0101490 phosphoglucosamine mutase

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



>NCBI__GCF_000381745.1:WP_019612989.1
          Length = 443

 Score =  204 bits (519), Expect = 5e-57
 Identities = 155/447 (34%), Positives = 225/447 (50%), Gaps = 33/447 (7%)

Query: 3   KLFGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61
           K FGT G+RG +    ITPEFA+K+G A G +L + G KK  V++G+D R+SG ML+ AL
Sbjct: 4   KYFGTDGIRGKVGASLITPEFALKLGWAAGRVLAKSGSKK--VLIGKDPRISGYMLEAAL 61

Query: 62  ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +GL + G   + +G  PTPAV + T  F A  G VI+ASHNP   NGIK     G  L 
Sbjct: 62  QAGLTAAGLRPVLMGPMPTPAVAYLTHTFRATAGIVISASHNPYYDNGIKFFSDKGTKLS 121

Query: 122 KEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKS----KVDVEAIKKRKPF 176
           ++ E  +E    KE        ++G+  R ED    YIE  KS    K D+  +K     
Sbjct: 122 EKVELEIEAEIDKE-LKCVDSSQLGKAYRIEDAAGRYIEFCKSTFPTKYDLSGLK----- 175

Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGA 236
           +VVD +NGA     P ++ ELG KVI++  +P+G     N      +++   E V    A
Sbjct: 176 IVVDCANGATYHIAPLVINELGAKVISMGVEPNGV--NINLNCGATSMQALSERVVKEKA 233

Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKE---KGGGLLVTTVATSNLLDD 293
           D+G+A DGD DR + +D  G  + GD+   ++A   L+    KGG   V T  ++  L+ 
Sbjct: 234 DYGIAFDGDGDRVMMVDHTGYILDGDELLYIIARDKLRTGTLKGGA--VGTKMSNLGLEQ 291

Query: 294 IAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIF 353
             K  G    R+ VGD  V   + +NN  IG E +G VI  + +   DG ++  +V+   
Sbjct: 292 ALKTLGIPFERSDVGDRHVMELMNKNNWCIGAENSGHVICSDLLPTGDGIVSGLQVMSAM 351

Query: 354 AKSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNK--VAEMARERGYTVDTTDGAKIIF 411
             S     EL   + KY Q+        +   + +K  +AE  R             ++ 
Sbjct: 352 QGSRMTLHELRQGMKKYPQVLLNVRFNNEIDPLQDKDILAEQKRIE----------DLLG 401

Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEK 438
           E G VL+R SGTEP+ R+  EA  KE+
Sbjct: 402 ERGRVLLRKSGTEPVFRVMVEADDKEE 428


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: 511
Number of extensions: 29
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: 443
Length adjustment: 33
Effective length of query: 422
Effective length of database: 410
Effective search space:   173020
Effective search space used:   173020
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