GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate Echvi_2982 Echvi_2982 Phosphomannomutase

Query= SwissProt::P18159
         (581 letters)



>FitnessBrowser__Cola:Echvi_2982
          Length = 575

 Score =  446 bits (1148), Expect = e-130
 Identities = 233/543 (42%), Positives = 339/543 (62%), Gaps = 15/543 (2%)

Query: 15  HLDLELKERLIEL--EGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGF 72
           ++D E K ++ +L    D   L D FYKDLEFGTGG+RG +G G+NRMN+YTV  A+ G 
Sbjct: 17  NIDQESKTKIQQLLDASDSSELVDAFYKDLEFGTGGLRGVMGIGSNRMNVYTVGMATQGL 76

Query: 73  AAYISK--QGEEAKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSF 130
           A Y+     GE+ K   V I +DSR  +  FA   A  L   GI+   F+E+RPTP LS+
Sbjct: 77  ANYLLACFPGEDIK---VAITHDSRINNTLFAETTANVLTANGIKVKYFEEMRPTPMLSY 133

Query: 131 AVRQLNAYGGIVVTASHNPPEYNGYKVYGDDGGQLPPKEADIVIEQVNAIENELTITVDE 190
           A+R      G+++TASHNP EYNGYK Y +DGGQ+       +I +V  I++     +D+
Sbjct: 134 AIRHYGCKSGVMITASHNPKEYNGYKAYWEDGGQIVAPHDKNIIMEVQKIKS-----IDD 188

Query: 191 ENKLKEKGLIKIIGEDIDKVYTEKLTSISVHPE-LSEEVDVKVVFTPLHGTANKPVRRGL 249
               K   LI+ IG ++D  Y   +   S+ P+ +  + D+ +VF+P+HG + K V   L
Sbjct: 189 VKWDKNDALIEYIGAEMDLTYLNDIKKFSLSPKAILNQRDMCIVFSPIHGASGKMVPAAL 248

Query: 250 EALGYKNVTVVKEQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRL 309
           +  G++N+ VVKEQE PD  F TV  PNPEE  A   ++KL +E NA++++A DPD DR 
Sbjct: 249 KTFGFENIHVVKEQEAPDGTFPTVVYPNPEEAEALSLSLKLAKEVNAELVLACDPDGDRY 308

Query: 310 GIAVKNDQGKYTVLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSF 369
             A+ N++G+Y +L GNQTG++L +YLL++ ++ G+   +  ++ TIVT+E+   +   F
Sbjct: 309 AAAIPNEKGEYELLNGNQTGSILTYYLLNQWREHGLFTGDQFMVNTIVTTELIEEICHGF 368

Query: 370 GLDTIDTLTGFKFIGEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQAALLAVEV 429
            +     LTGFK I   I+E E  G+  F  G EESYG+L+GD  RDKD + A  +  EV
Sbjct: 369 NIPCYRVLTGFKNIAAIIRELE--GKKQFVGGGEESYGFLVGDAVRDKDGVSACAMLAEV 426

Query: 430 CAFYKKQGMSLYEALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAG 489
            A+YK++GM+L++ L  ++  YGFY+E L S+T KGK GAEQI+ ++  FR N P+ + G
Sbjct: 427 VAYYKEKGMTLFDVLAEIYQSYGFYKESLISVTKKGKDGAEQIQQLMHGFRTNRPEAING 486

Query: 490 KQVVTAEDYAVSKRTLLTESKEEAIDLPKSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAV 549
            +VV   D   SK   + +  EE +DL KSNV++++LEDGS    RPSGTEPK+K+Y +V
Sbjct: 487 TKVVKVVDVKESKVYNIADGTEEDLDLDKSNVIQFYLEDGSKISARPSGTEPKIKYYISV 546

Query: 550 KGS 552
             S
Sbjct: 547 NES 549


Lambda     K      H
   0.313    0.133    0.371 

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: 829
Number of extensions: 35
Number of successful extensions: 4
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: 581
Length of database: 575
Length adjustment: 36
Effective length of query: 545
Effective length of database: 539
Effective search space:   293755
Effective search space used:   293755
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 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