Alignments for a candidate for sdh in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Pseudomonas stutzeri RCH2

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate GFF2858 Psest_2914 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::Q70JN9
         (743 letters)



>FitnessBrowser__psRCH2:GFF2858
          Length = 776

 Score =  463 bits (1191), Expect = e-134
 Identities = 252/661 (38%), Positives = 365/661 (55%), Gaps = 30/661 (4%)

Query: 83  DIGSMDPNDVPQMAPQQSASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHT 142
           DI  M P  + Q AP    S  +GDW AYG      RYSPL++ITPQN D+L+  + Y T
Sbjct: 141 DIKGMLPAPLAQ-APAADDSVPAGDWHAYGRSQHGQRYSPLAQITPQNVDRLEPVWHYQT 199

Query: 143 GSYPRPGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYT 202
           G    P   ++   E TP+KV D LY+C+  N ++ +D  TG+E WR +    +      
Sbjct: 200 GDLRGPDDPDETTYEVTPLKVDDSLYLCTPHNLVIALDAETGQERWRFDPKVPHSVNRQH 259

Query: 203 AACKGVTYFTSSQVPEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLG 262
             C+G++Y  + Q  + Q C  R+   T D RLIA+DA TG +C GF + G+++L   + 
Sbjct: 260 LTCRGLSYHAAPQGSDVQACRQRLFMPTADARLIALDAKTGEICPGFADNGEIDLWANMP 319

Query: 263 ESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPND 322
            +  GF   T+PP V   +V++   V D  R   PSGVIR YD  +G+  W WD   P+ 
Sbjct: 320 HAKEGFYYSTSPPVVARDLVIIGGAVNDNVRAQEPSGVIRAYDVYTGQLKWNWDPGNPDA 379

Query: 323 HSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVAL 382
                    YS  +PNSW+  + D ALG+VYVP GN   D +   R+    + SS++VAL
Sbjct: 380 TEPIAAGQTYSPSSPNSWSISSADEALGMVYVPLGNQVPDQWGGRRNENSERFSSSIVAL 439

Query: 383 DVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDG 442
           D+ +G  RWVFQTV  D+WD D+ +Q +L+D+  ++G PVPA++ PTK+G  +VLDRR G
Sbjct: 440 DLDSGQLRWVFQTVRHDLWDMDVPAQPSLVDIQTENG-PVPAVVAPTKQGDIYVLDRRTG 498

Query: 443 KPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPIDQLFCRIKF 502
           +PILPV E PAP  G   GD  + TQP S    +   P L+  D+WG + IDQ+ C I+F
Sbjct: 499 EPILPVREVPAPQ-GAAEGDWVAKTQPASA--LSYEPPKLQGKDLWGATLIDQMMCHIQF 555

Query: 503 RRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRKK 562
               Y G +TPPS     + +PG  G  +WG V+ DP   ++ +         +L+ R+ 
Sbjct: 556 HSLRYEGRYTPPSTQGTLV-HPGNFGVFNWGGVAVDPVRQMVFSTPAYLAFTSKLIPRED 614

Query: 563 ADELGLM---PIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMIT 619
           A+   +    P  + N+              G+P+ + +  F     G+ C  PP+G + 
Sbjct: 615 AETTYVSEQEPFLNENF--------------GSPFAVELKAFVSP-IGLPCTAPPWGYVA 659

Query: 620 AIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQ 679
             D++ G K  W    GT R   P  +P  LP+++G PN GG ++TAGGV F++   D  
Sbjct: 660 GADLRTG-KTHWLRKNGTVRDRSP--IP--LPFKMGVPNLGGPMLTAGGVAFLSGTLDYY 714

Query: 680 IRAIDEHTGKVVWSAVLPGGGQANPMTYEA-NGHQYVAIMAGGHHFMMTPVSDQLVVYAL 738
           +RA D  TG+ +W A LP GGQA PMTY++ +G Q V ++AGGH  + T   D ++ YAL
Sbjct: 715 LRAYDVMTGRELWKARLPAGGQATPMTYQSRSGRQMVVVVAGGHGSLGTKAGDSVIAYAL 774

Query: 739 P 739
           P
Sbjct: 775 P 775


Lambda     K      H
   0.315    0.134    0.428 

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: 2049
Number of extensions: 149
Number of successful extensions: 11
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: 743
Length of database: 776
Length adjustment: 40
Effective length of query: 703
Effective length of database: 736
Effective search space:   517408
Effective search space used:   517408
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: 42 (22.0 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources