GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Methanobacterium arcticum M2

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_048080780.1 EI99_RS04680 hypothetical protein

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



>NCBI__GCF_000746075.1:WP_048080780.1
          Length = 431

 Score =  249 bits (636), Expect = 1e-70
 Identities = 146/434 (33%), Positives = 227/434 (52%), Gaps = 21/434 (4%)

Query: 10  VRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALISGLLSVG 69
           +RG+ N +IT EFA  +G   G  + R G+K   V+VGRD     +M+K ++ +G+L+ G
Sbjct: 8   IRGVVNSEITNEFASNLGNIIGNFV-RSGKK---VIVGRDINDPSQMIKRSITAGILAAG 63

Query: 70  CDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKEREAIVE 129
            DVID GIAP P V +    +N D    ITASH  PE   IK+   + + L +       
Sbjct: 64  IDVIDFGIAPIPTVHYGADLYNTDVLVTITASHMNPEEIDIKVFSNHEIPLTQRHA---- 119

Query: 130 ELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVVVDTSNGAGSL 188
                   ++  W ++G++    D +  Y+ A+    +   I  R P VV+D +NG+   
Sbjct: 120 --------EKVSWDKVGQLSYVHDYVDKYLNAVLENTEKNVISSRAPKVVIDCANGSAVQ 171

Query: 189 TLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVAQDGDADR 248
            LP +L  LGC VI    QP      +  EP  E++     +V A+GAD G+A D D DR
Sbjct: 172 FLPEILSRLGCDVILFGCQPTNVSTKKFAEPTPESVSLVSNLVNAVGADMGIAMDNDGDR 231

Query: 249 AVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHGAKVMRTKVG 308
            +FIDE G  I+     A++A   L E   G +V++V  S  LD+I    G K+++  + 
Sbjct: 232 VIFIDEKGNVIRDQTVLAILAREALIENPEGTIVSSVTASMSLDEIVSDQGGKLLKAPMN 291

Query: 309 DLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKFSELIDELP 368
              V   + +N    GG+++G  +FP+     D      K++EI  K  K FS L++E+P
Sbjct: 292 --CVLDEIIKNKAVFGGDDSGMYVFPQFQECFDAIFAAVKMLEIICKHNKTFSTLVNEIP 349

Query: 369 KYYQIKTKRHVEGD-RHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLVRASGTEPII 427
           +Y +     + E D +  ++  + E  +E G  +DTT+G K+  ED +VLVR S  EP++
Sbjct: 350 EYPRTVFSVNCEHDEKQKVLTNLEENLKENG-EIDTTEGIKMQEEDSFVLVRPSRFEPLL 408

Query: 428 RIFSEAKSKEKAQE 441
           R++ EAKS  K Q+
Sbjct: 409 RVYVEAKSSGKLQK 422


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: 477
Number of extensions: 24
Number of successful extensions: 5
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: 431
Length adjustment: 32
Effective length of query: 423
Effective length of database: 399
Effective search space:   168777
Effective search space used:   168777
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