GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Shewanella amazonensis SB2B

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate 6936771 Sama_0956 phosphoglucosamine mutase (RefSeq)

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



>lcl|FitnessBrowser__SB2B:6936771 Sama_0956 phosphoglucosamine
           mutase (RefSeq)
          Length = 445

 Score =  223 bits (568), Expect = 1e-62
 Identities = 159/453 (35%), Positives = 235/453 (51%), Gaps = 33/453 (7%)

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   KFFGTDGIRGKVGADQMTPELALKLGWAAGRVLARTGTKK--VIIGKDTRISGYMFESAL 62

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

Query: 122 KEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVVVD 180
            E E  + E   ++    A+   +G+V R +D    YIE  K     +        +VVD
Sbjct: 123 DEIELAI-EAELEKPLICAESQFLGKVSRIDDARGRYIEYCKGNFPADQTLSGLK-IVVD 180

Query: 181 TSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGV 240
            ++GA     P + RELG +V+ +  +P+G     N +    ++    + V  + AD G+
Sbjct: 181 CAHGATYHIAPAVFRELGAEVVAIGVEPNGM--NINDKCGATSMGAIRDKVLEVNADLGI 238

Query: 241 AQDGDADRAVFIDENGRFIQGDK-TFALVADAVLKEKG---GGLLVTTVATSNLLDDIAK 296
           A DGD DR + + + G  I GD+  + L  DA  KE+G   GG++ T +A    L+   K
Sbjct: 239 ALDGDGDRIMMVTQEGDIIDGDQILYILALDA--KERGLLKGGVVGTQMANLG-LELALK 295

Query: 297 KHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKS 356
             G    R+KVGD  V   L E    IGGE +G ++  +H    DG +    V+    +S
Sbjct: 296 DEGIPFARSKVGDRYVMELLKELGWRIGGENSGHILNLDHGTTGDGIVAGILVLAAMRRS 355

Query: 357 GKKFSELIDELPKYYQIKTKRHVEGDRH-----AIVNKVAEMARERGYTVDTTDGAKIIF 411
           GK   +LI +L  + Q+      EGD++      +  KVAE+ RE G             
Sbjct: 356 GKGLQQLIAKLKMFPQVLVNVRFEGDKNPLEADTVTAKVAEVERELG------------- 402

Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLN 444
           E G VL+R SGTEP++R+  E + KE      N
Sbjct: 403 ERGRVLLRKSGTEPLLRVMVEGEDKETVTRLAN 435


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: 509
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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