GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Shewanella oneidensis MR-1

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate 200379 SO1199 phosphoglucosamine mutase (NCBI ptt file)

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



>FitnessBrowser__MR1:200379
          Length = 445

 Score =  199 bits (507), Expect = 1e-55
 Identities = 146/454 (32%), Positives = 229/454 (50%), Gaps = 17/454 (3%)

Query: 3   KLFGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61
           K FGT G+RG + + ++TPE A+K+G A G +L R G KK  V++G+DTR+SG M + AL
Sbjct: 5   KFFGTDGIRGKVGSGQMTPELALKLGWAAGRVLSRSGTKK--VIIGKDTRISGYMFESAL 62

Query: 62  ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +GL + G +V+ +G  PTPAV + T+ F A+ G VI+ASHNP   NGIK    +G  L 
Sbjct: 63  EAGLSAAGLNVMLMGPMPTPAVAYLTRTFRAEAGVVISASHNPYYDNGIKFFSTDGSKLD 122

Query: 122 KEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVVVD 180
              E  + E   ++     + + +G+V R ED    YIE  K     +        +VVD
Sbjct: 123 DNLELEI-EAELEKPLVCVESHLLGKVSRIEDARGRYIEYCKGNFPADQTLTGLK-IVVD 180

Query: 181 TSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGV 240
            ++GA     P + RELG +VI +  +P+G     N +    ++ +  E V A  AD G+
Sbjct: 181 CAHGATYHIAPAVFRELGAEVIAIGDKPNGV--NINDKVGATSMAKICETVLAETADLGI 238

Query: 241 AQDGDADRAVFIDENGRFIQGDK-TFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHG 299
           A DGD DR + ++  G  I GD+  + L  DA  +    G +V T+ ++  LD   +   
Sbjct: 239 ALDGDGDRIMMVNSKGEVIDGDQILYILACDAKARGVLRGGVVGTLMSNLGLDLALQALD 298

Query: 300 AKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKK 359
               R+KVGD  V   L E +  IGGE +G ++  +H    DG +    V+    +    
Sbjct: 299 IPFARSKVGDRYVMELLKELDWRIGGENSGHILNLDHGTTGDGIVAGILVLAAMRRQNAT 358

Query: 360 FSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLVR 419
             +L   +    Q+      EG+   + +   + A+ +   V++  G +     G VL+R
Sbjct: 359 LEQLTAPMEMLPQVLVNVRFEGEHDPLSSDKVKAAQAQ---VESELGVR-----GRVLLR 410

Query: 420 ASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKA 453
            SGTEP+IR+  E         + NL  + ++ A
Sbjct: 411 KSGTEPLIRVMVEGDDHNTVLAHANLIADAVKSA 444


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: 474
Number of extensions: 31
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: 445
Length adjustment: 33
Effective length of query: 422
Effective length of database: 412
Effective search space:   173864
Effective search space used:   173864
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