GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolJ in Rhodobacter viridis JA737

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate WP_110806485.1 C8J30_RS14070 5-dehydro-2-deoxygluconokinase

Query= reanno::Caulo:CCNA_01356
         (642 letters)



>NCBI__GCF_003217355.1:WP_110806485.1
          Length = 638

 Score =  658 bits (1698), Expect = 0.0
 Identities = 353/631 (55%), Positives = 417/631 (66%), Gaps = 5/631 (0%)

Query: 6   KTLDLIAVGRSSVDLYGQQVGGRLEDMGSFAKYLGGSPTNTAAGGARLGLKTGLLTRVGA 65
           KTLD+I +GR+ VDLYG QVGGRLEDMGSF KY+GGSPTN A G ARLGL++ L+TRVG 
Sbjct: 2   KTLDVITIGRAGVDLYGTQVGGRLEDMGSFQKYIGGSPTNIACGTARLGLRSALITRVGD 61

Query: 66  DHMGRFIREQLEREGVDVAGVLSDPDRLTALVILGIRDRVNFPLIFYRENCADMALEPSD 125
           +HMGRFIREQL REGVDV GV +DP+RLTALVILGIRD   FPLIFYRENCADMAL  +D
Sbjct: 62  EHMGRFIREQLGREGVDVRGVKTDPERLTALVILGIRDEEQFPLIFYRENCADMALCEAD 121

Query: 126 VDEAWFAQAGAVLINGTHLSQPNVYETSLKAARAVKAAGGRVAFDIDYRPVLWGLTGKDA 185
           ++E + A+A +VL  GTHLS P      LKA    +  G + A DIDYRP LWG+ G  A
Sbjct: 122 IEEGFIAEARSVLATGTHLSHPRTEAAVLKALALARKHGAKTALDIDYRPNLWGVAGHGA 181

Query: 186 GENRFVENQQVTAKLQEVVALCDLIVGTEEEIHILGGSTDTIAALRAIRRASDALLVCKR 245
           GE+RFVE+ +VTAKL   + L DLIVGTEEE HI GGSTDTIAALRA+R  S+A LVCKR
Sbjct: 182 GESRFVESAKVTAKLLGTLHLFDLIVGTEEEFHIAGGSTDTIAALRAVRAVSNATLVCKR 241

Query: 246 GPEGCVAFPGAIPDALDEGVSARGFKVEVFNVLGAGDAFMAGFLRGWLRHESVETCCEWG 305
           G +G VAF G IPD+LD+G S  GF +EVFNVLGAGD F +G L+GWL  E+     E+ 
Sbjct: 242 GAKGAVAFEGTIPDSLDDGQSGPGFPIEVFNVLGAGDGFFSGLLKGWLDGEAWPRALEYA 301

Query: 306 NACGAIVVSRHGCTPAMPTWIELQAFLSERERPFRLREDAELEHIHWATTRERVYDELTV 365
           NACGA  VSRHGCTPA P+  EL+ FL        LR DAELE +HWATTR+  +  + V
Sbjct: 302 NACGAFAVSRHGCTPAYPSLEELKFFLRRGVVRPDLRNDAELEQVHWATTRKGDWSTMRV 361

Query: 366 LAIDHRSQFEDLIAETGGDAERIPDFKRLALRAVQMVAGRDETRFGMLLDGRFGFEALAE 425
            A DHR Q E L    G  A++   FK L L A + V G     +G+L D R G +AL  
Sbjct: 362 FAFDHRMQLEQL---PGFTADKGSRFKELCLAAAREVQG-GRPGYGILCDNRIGRKALHA 417

Query: 426 AADHDYWIARPIELPKSRPLEFECSADVATELLE-WPLNQVVKCLAFYHPDDESDLRERQ 484
           A+    WI RP E P SRPLE E         LE W    VVK L F HPDD  DLR  Q
Sbjct: 418 ASGTGLWIGRPCEWPGSRPLELEPELGPDCGGLENWARENVVKVLVFCHPDDAPDLRRAQ 477

Query: 485 ERQLLRLADACRKTRHELLLELILPRGMSSDSRTVARAIRRLYALGIRPDWWKLEPLTDP 544
           E +++RL  A R+ R E LLE+I  +       T A  IR+ YA G+ PDWWKLEP+   
Sbjct: 478 EAEVVRLYTAARRNRLEFLLEIIPSKVGPVTETTTATLIRQFYAAGVCPDWWKLEPMATR 537

Query: 545 DAWREIEIAIAENDPLCRGVVLLGLSAPEAELVASFEVVAPFPIVKGFAVGRTIFYDVAR 604
            AW     AI ENDP  RG+V+LGL APE +L  SF + A FP+VKGFAVGRTIF  VAR
Sbjct: 538 AAWAAACAAIEENDPHTRGIVVLGLDAPEEDLAESFAIAAGFPLVKGFAVGRTIFGVVAR 597

Query: 605 AWLSNQIDDDAAVTALAAKFKVLVDAWRRLR 635
           AW    + D  AV  +A ++  L   W R R
Sbjct: 598 AWFEGDLGDAEAVAEMARRYARLCTVWDRAR 628


Lambda     K      H
   0.322    0.138    0.419 

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: 1139
Number of extensions: 41
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: 642
Length of database: 638
Length adjustment: 38
Effective length of query: 604
Effective length of database: 600
Effective search space:   362400
Effective search space used:   362400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 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