GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas simiae WCS417

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate GFF2149 PS417_10960 quinate dehydrogenase

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__WCS417:GFF2149
          Length = 802

 Score =  592 bits (1526), Expect = e-173
 Identities = 328/809 (40%), Positives = 462/809 (57%), Gaps = 38/809 (4%)

Query: 7   GSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALW 66
           G  RLL+    +  AL GL L IGG  LV++GGSWY+ I G +M     ++   K A  W
Sbjct: 9   GVSRLLLLGLGVIIALLGLALAIGGVKLVSLGGSWYFLIGGAIMAIAGLLIACRKPAGAW 68

Query: 67  LYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVI-PASGAVAALV 125
           ++AA L+GT IW V +VG  FW L  R  + +F  I +++  V+  LV  PA GA A   
Sbjct: 69  VFAAFLIGTAIWAVADVGLVFWPLFSR--LFMFAAIGMVVALVYPLLVNKPARGAYA--- 123

Query: 126 VALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVA----DQDWPAYGRNQEGQRFS 181
           VA +++ G+   AG      +     A       I+PVA     +DW  YG  + G RF+
Sbjct: 124 VAAVLAAGVAVAAG---NMFVAHPSVAPTGAGPGITPVAAGDAQKDWAHYGNTEGGSRFA 180

Query: 182 PLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDA 241
            L QIN D V+ LK AW + TGDV   +  G   +++TP+++G+ +++CT H  L ALDA
Sbjct: 181 ALDQINRDTVNKLKVAWTYHTGDVAISDGNGA-EDQLTPLQIGNKVFICTPHNNLIALDA 239

Query: 242 ASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPE-------------VMADCPR 288
            +GKE W  +   K   S     CRG++Y +A A  A P                A C R
Sbjct: 240 DTGKELWKNEVNAK---SAVWQRCRGMAYFDATAPIAQPTQPNSSPIMPASVPAGAQCQR 296

Query: 289 RIILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVM 348
           R++    D RLIA++A+ GK CE F   G ++L++ + +     Y+ +S P+I   T+V+
Sbjct: 297 RLLTNTIDARLIAVDADTGKFCEDFGTHGQVDLKAGLGNVPDSYYQLSSAPLIAGTTVVV 356

Query: 349 AGSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAA 408
            G V DN  T    GVIRGFDV +G++ WAFDPG  +    P+D  T+  ++PNSWAP +
Sbjct: 357 GGRVADNVQTDMPGGVIRGFDVISGQMRWAFDPGNPEDKQAPADGSTYVRSTPNSWAPMS 416

Query: 409 YDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMD 468
           YD  ++ V+LPMG ++ DI+G  RT    +Y +S+LAL+A+TG   W YQTVH+DLWD D
Sbjct: 417 YDPLMNTVFLPMGSSSTDIYGVERTQLNHKYGASVLALDASTGAEKWVYQTVHNDLWDFD 476

Query: 469 LPAQPTLADITVNG--QKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYV 526
           LP QP+L D T  G  + VP +    K G I+VLDR  G+ +    E PV       +  
Sbjct: 477 LPMQPSLIDFTPPGSDKAVPAVVIGTKAGQIYVLDRATGKPLTDVQEVPVKAANIPNEPY 536

Query: 527 TPTQPFS-ELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPG 585
           +PTQP S  +     + L+ +DMWGAT FDQL+CR+ F  MRYEG++T P    +L FPG
Sbjct: 537 SPTQPKSVGMPQIGAQTLTESDMWGATPFDQLLCRIDFKGMRYEGLYTAPGTDKSLSFPG 596

Query: 586 NLGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQY 645
           +LG   WG IS DP       N M L    +++P    N  +     +   T  G  P  
Sbjct: 597 SLGGMNWGSISTDPVHGFIFVNDMRLGLWIQMVP--SQNKAQASSGGEALNTGMGAVPLK 654

Query: 646 GVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPF 705
           G PY V  N FLS  G+PC+ P +G ++A+D+KT +V W+  +GT +D+ P  + + +P 
Sbjct: 655 GTPYAVNKNRFLSVAGIPCQAPPFGTLTAIDMKTQKVAWQVPVGTVEDTGPLGIRMHLPI 714

Query: 706 NMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY--EVN 763
            +G+P LGG +ST G ++FIA T D YLRA+N  NG+++W+ RLP G Q  PMTY     
Sbjct: 715 KIGLPTLGGTLSTQGGLIFIAGTQDFYLRAFNSGNGDEVWKARLPVGSQGGPMTYVSPKT 774

Query: 764 GKQYVVISAGGHGSFGTKMGDYIVAYALP 792
           GKQY+VI+AGG     T  GDY++AYALP
Sbjct: 775 GKQYIVITAGG-ARQSTDRGDYVIAYALP 802


Lambda     K      H
   0.319    0.137    0.436 

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: 2135
Number of extensions: 145
Number of successful extensions: 12
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: 796
Length of database: 802
Length adjustment: 41
Effective length of query: 755
Effective length of database: 761
Effective search space:   574555
Effective search space used:   574555
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 (21.7 bits)
S2: 55 (25.8 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