Alignments for a candidate for gdh in Algoriphagus machipongonensis PR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Algoriphagus machipongonensis PR1

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_008203192.1 ALPR1_RS19260 PQQ-binding-like beta-propeller repeat protein

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_000166275.1:WP_008203192.1
          Length = 705

 Score =  239 bits (611), Expect = 3e-67
 Identities = 165/481 (34%), Positives = 235/481 (48%), Gaps = 55/481 (11%)

Query: 163 SNIADGDWPAYARDQQGTRFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTP 222
           +NI   DW  Y   + G+R+S L QIN DNV +L  AW + TGD    S       +  P
Sbjct: 23  NNIDYTDWSHYGGPEDGSRYSSLTQINKDNVSQLAQAWVYHTGDATERSQI-----QCQP 77

Query: 223 IKIRDTLYLCTPHQILFALDAATGKQKWKFDP-GLKTNPTFQHVTCRGVSYHEFPAAKDA 281
           I I   LY  +P   +FALDAATGK+ W+FDP  +         T RGVSY  +  A+D 
Sbjct: 78  IVIDGILYGTSPSLDVFALDAATGKEIWRFDPFDILGGENSWAGTNRGVSY--WAEAED- 134

Query: 282 SNTQPALCSRRIYLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPG-MYEPTS 340
                    +RI     +  L A+DA TG     FG+ G++DL+          +    +
Sbjct: 135 ---------KRILFGAGNW-LMAVDALTGNPISEFGDGGKVDLRKNLDTDRDDFLIVANA 184

Query: 341 PPVITDTTIVMAGAVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPA------ 394
           P VI    I++   +++        G IR ++V TGK  W+F       + IP       
Sbjct: 185 PGVIFKDKIIIGMRLSEGLDAAP--GHIRAYNVKTGKREWIF-------HTIPQKGEFGY 235

Query: 395 ----DEHTFTMNSPNSWAPAVYDPKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALN 450
                E    +   N+WA  V D K +IV++P G  T D WGG RT +   YA+S++AL+
Sbjct: 236 DTWDSEFIQKIGGANNWAGMVVDQKREIVFVPTGSATYDFWGGYRTGDN-LYANSLVALD 294

Query: 451 ATTGKLVWSYQTVHHDLWDMDLPSQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGK 510
           A TG+ +W +Q VHHD+WD D P+ P L  I  K+G  +  +   +K G  +V DR +G+
Sbjct: 295 ANTGERIWHFQAVHHDVWDRDFPANPNLIRI-QKEGEWIDAVAQISKQGMTYVFDRESGE 353

Query: 511 TVVPAPETPVPQGAAKGDHVSATQ-------PYSELTFRPKQNLTDKDMWGATMYDQLVC 563
            + P  ET VPQ    G+  SATQ       P+  +TF     L+ K  W   +  QLV 
Sbjct: 354 PIWPIVETNVPQSNLPGEITSATQPIPTLPEPFMNMTFEDSDILSLKPEWEEDIRSQLV- 412

Query: 564 RVIFKRLRYEGPFTPP-SEQGTLVFPGNLGMFEWGGISVDPHRQIAIANPMALPFVSKLI 622
                 ++Y   + PP SE G ++FPG  G  EWGG S DP  Q    N   +P++ ++ 
Sbjct: 413 -----NVQYGDTWAPPSSEHGIILFPGMDGGGEWGGASFDPSNQTLYVNANQIPWLIEMT 467

Query: 623 P 623
           P
Sbjct: 468 P 468



 Score =  115 bits (288), Expect = 8e-30
 Identities = 60/133 (45%), Positives = 80/133 (60%), Gaps = 3/133 (2%)

Query: 662 LSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKMGMPMLGGPVATAG 721
           L+  G+    P WG ++A+D+ T +  W+  +G +   S        G    GGPV TAG
Sbjct: 576 LTKDGVYGSNPPWGLLTAIDMNTGKKKWQVTLGEINSLSAQGFE-PTGTENYGGPVVTAG 634

Query: 722 KVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTYEVNGKQYVVIAAGGHGSFGT 781
            + FI AT D  +RAF  +TGE LW+A+LPA G ATP  YE +GKQ++VIA G  G  GT
Sbjct: 635 GLLFIAATKDEKIRAFDKETGEKLWEAKLPAAGHATPAMYEYDGKQFLVIACG--GGKGT 692

Query: 782 KLGDYVIAYALPD 794
           K GD  +A+ALPD
Sbjct: 693 KSGDSYVAFALPD 705



 Score = 29.6 bits (65), Expect = 6e-04
 Identities = 35/134 (26%), Positives = 50/134 (37%), Gaps = 26/134 (19%)

Query: 210 PSDPGEITDEVTPIKIRDTLYLCTPHQ-ILFALDAATGKQKWKFDPGLKTNPTFQHVTCR 268
           P  PG   +    +  +D +Y   P   +L A+D  TGK+KW+   G   + + Q     
Sbjct: 562 PLAPGYYMNGYKKLLTKDGVYGSNPPWGLLTAIDMNTGKKKWQVTLGEINSLSAQGFEPT 621

Query: 269 GVSYHEFPAAKDASNTQPALCSRRIYLPVNDGRLFALDAETGE-----RCPAFGNNGELD 323
           G   +  P       T   L          D ++ A D ETGE     + PA G+     
Sbjct: 622 GTENYGGPVV-----TAGGLL---FIAATKDEKIRAFDKETGEKLWEAKLPAAGH----- 668

Query: 324 LQHKQPVTTPGMYE 337
                   TP MYE
Sbjct: 669 -------ATPAMYE 675



 Score = 28.9 bits (63), Expect = 0.001
 Identities = 25/83 (30%), Positives = 33/83 (39%), Gaps = 14/83 (16%)

Query: 300 GRLFALDAETGERC--PAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTD 357
           G L A+D  TG++      G    L  Q  +P  T    E    PV+T   ++   A  D
Sbjct: 589 GLLTAIDMNTGKKKWQVTLGEINSLSAQGFEPTGT----ENYGGPVVTAGGLLFIAATKD 644

Query: 358 NFSTREPSGAIRGFDVNTGKLLW 380
                     IR FD  TG+ LW
Sbjct: 645 E--------KIRAFDKETGEKLW 659


Lambda     K      H
   0.319    0.137    0.433 

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: 1853
Number of extensions: 144
Number of successful extensions: 22
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 6
Number of HSP's successfully gapped: 4
Length of query: 796
Length of database: 705
Length adjustment: 40
Effective length of query: 756
Effective length of database: 665
Effective search space:   502740
Effective search space used:   502740
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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