GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Shewanella loihica PV-4

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate 5210391 Shew_2832 phosphoglucosamine mutase (RefSeq)

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



>FitnessBrowser__PV4:5210391
          Length = 443

 Score =  211 bits (538), Expect = 3e-59
 Identities = 154/460 (33%), Positives = 235/460 (51%), Gaps = 29/460 (6%)

Query: 1   MGKLFGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKE 59
           M K FGT G+RG +   K+TPE A+K+G A G +L R G KK  V++G+DTR+SG + + 
Sbjct: 1   MRKFFGTDGIRGKVGAGKMTPELALKLGWAAGRVLSRTGTKK--VIIGKDTRISGYLFES 58

Query: 60  ALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMG 119
           A+ +GL + G +V+ +G  PTPAV + T+ F A+ G VI+ASHNP   NGIK    +G  
Sbjct: 59  AMEAGLSAAGLNVMLMGPMPTPAVAYLTRTFRAEAGVVISASHNPYYDNGIKFFSTDGSK 118

Query: 120 LKKEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVE-AIKKRKPFV 177
           L  E E  +E    ++  +  + + +G+V R ED    YIE  K     E  +   K  +
Sbjct: 119 LDDEVELEIER-ELEKPLECVESHLLGKVSRIEDAAGRYIEYCKGNFPAEHTLNGLK--I 175

Query: 178 VVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGAD 237
           VVD ++GA     P + RELG +VIT+  +PDG     N E    ++ +  E V A  AD
Sbjct: 176 VVDCAHGATYHIAPSVFRELGAEVITIGDKPDGI--NINHEVGATSMGKIRETVIAEKAD 233

Query: 238 FGVAQDGDADRAVFIDENGRFIQGDK-TFALVADAVLKEKGGGLLVTTVATSNLLDDIAK 296
            G+A DGD DR + ++ +G+ I GD+  + L  DA  +    G +V T+ ++  LD   K
Sbjct: 234 LGIALDGDGDRIMMVNRHGKVIDGDEILYILACDAQDRGVLKGGVVGTLMSNLGLDLALK 293

Query: 297 KHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKS 356
                  R+KVGD  V   L E +  IGGE +G ++  +H    DG +    V+    + 
Sbjct: 294 ARDIPFARSKVGDRYVMELLKEKDWRIGGENSGHILNLDHGTTGDGIVAGILVLAAMCRK 353

Query: 357 GKKFSELIDELPKYYQIKTKRHVEG-----DRHAIVNKVAEMARERGYTVDTTDGAKIIF 411
                EL + +    Q+      EG     +  ++++  AE+  + G             
Sbjct: 354 QATLEELTEGIKMLPQVLVNVRFEGTHNPLEADSVLSAQAEVEAKLG------------- 400

Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLE 451
           E G VL+R SGTEP+IR+  E       + + N   E ++
Sbjct: 401 ERGRVLLRKSGTEPLIRVMVEGDVASDVKAHANYIAEAIK 440


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: 519
Number of extensions: 30
Number of successful extensions: 7
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 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