Alignments for a candidate for etoh-dh-c in Algoriphagus machipongonensis PR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Algoriphagus machipongonensis PR1

Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate WP_008203192.1 ALPR1_RS19260 PQQ-binding-like beta-propeller repeat protein

Query= CharProtDB::CH_107432
         (595 letters)



>NCBI__GCF_000166275.1:WP_008203192.1
          Length = 705

 Score =  135 bits (340), Expect = 6e-36
 Identities = 108/345 (31%), Positives = 163/345 (47%), Gaps = 48/345 (13%)

Query: 53  GQRYSPLDLLNANNVKELRPVWAFSFGGEKQRGQ-QAQPLIKDGVMYLTGSYSRVFAVDA 111
           G RYS L  +N +NV +L   W +  G   +R Q Q QP++ DG++Y T     VFA+DA
Sbjct: 39  GSRYSSLTQINKDNVSQLAQAWVYHTGDATERSQIQCQPIVIDGILYGTSPSLDVFALDA 98

Query: 112 RTGKKLWQYDARLPDDI---RPCCDVINRGVALYGDL----VFFGT---------LDAKL 155
            TGK++W++D   P DI          NRGV+ + +     + FG          L    
Sbjct: 99  ATGKEIWRFD---PFDILGGENSWAGTNRGVSYWAEAEDKRILFGAGNWLMAVDALTGNP 155

Query: 156 VALNKDTGKVVWSKKVADHKEGYSISA-AP-MIVNGKLITGV--AGGEFGVVGKIQAYNP 211
           ++   D GKV   K +   ++ + I A AP +I   K+I G+  + G     G I+AYN 
Sbjct: 156 ISEFGDGGKVDLRKNLDTDRDDFLIVANAPGVIFKDKIIIGMRLSEGLDAAPGHIRAYNV 215

Query: 212 ENGELLWMRPTV--EGHMGYVYKDGKAIENGISGGEAGKTWPGDLWKTGGAAPWLGGYYD 269
           + G+  W+  T+  +G  GY   D + I+                 K GGA  W G   D
Sbjct: 216 KTGKREWIFHTIPQKGEFGYDTWDSEFIQ-----------------KIGGANNWAGMVVD 258

Query: 270 PETNLILFGTGNPAP--WNSHLRPGDNLYSSSRLALNPDDGTIKWHFQSTPHDGWDFDGV 327
            +  ++   TG+     W  + R GDNLY++S +AL+ + G   WHFQ+  HD WD D  
Sbjct: 259 QKREIVFVPTGSATYDFWGGY-RTGDNLYANSLVALDANTGERIWHFQAVHHDVWDRDFP 317

Query: 328 NELISFNYKDGGKEVKAAATADRNGFFYVLDRTNGKFIRGFPFVD 372
                   +  G+ + A A   + G  YV DR +G+ I  +P V+
Sbjct: 318 ANPNLIRIQKEGEWIDAVAQISKQGMTYVFDRESGEPI--WPIVE 360



 Score = 51.2 bits (121), Expect = 1e-10
 Identities = 30/101 (29%), Positives = 54/101 (53%), Gaps = 15/101 (14%)

Query: 470 GVLRAIDPISGKEVWR----------HKNYAPL----WGGVLTTKGNLVF-TGTPEGFLQ 514
           G+L AID  +GK+ W+           + + P     +GG + T G L+F   T +  ++
Sbjct: 589 GLLTAIDMNTGKKKWQVTLGEINSLSAQGFEPTGTENYGGPVVTAGGLLFIAATKDEKIR 648

Query: 515 AFNAKTGDKVWEFQTGSGVLGSPVTWEMDGEQYVSVVSGWG 555
           AF+ +TG+K+WE +  +    +P  +E DG+Q++ +  G G
Sbjct: 649 AFDKETGEKLWEAKLPAAGHATPAMYEYDGKQFLVIACGGG 689



 Score = 36.6 bits (83), Expect = 4e-06
 Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 7/88 (7%)

Query: 91  LIKDGVMYLTGSYSRVFAVDARTGKKLWQ-----YDARLPDDIRPC-CDVINRGVALYGD 144
           L KDGV      +  + A+D  TGKK WQ      ++       P   +     V   G 
Sbjct: 576 LTKDGVYGSNPPWGLLTAIDMNTGKKKWQVTLGEINSLSAQGFEPTGTENYGGPVVTAGG 635

Query: 145 LVFF-GTLDAKLVALNKDTGKVVWSKKV 171
           L+F   T D K+ A +K+TG+ +W  K+
Sbjct: 636 LLFIAATKDEKIRAFDKETGEKLWEAKL 663



 Score = 32.3 bits (72), Expect = 7e-05
 Identities = 53/235 (22%), Positives = 85/235 (36%), Gaps = 32/235 (13%)

Query: 302 ALNPDDGTIKWHFQSTPHDGWD--FDGVNELISFNYKDGGKEVKAAATADRNGFFYVLDR 359
           AL+   G   W F      G +  + G N  +S+  +   K +   A      +   +D 
Sbjct: 95  ALDAATGKEIWRFDPFDILGGENSWAGTNRGVSYWAEAEDKRILFGA----GNWLMAVDA 150

Query: 360 TNGKFIRGFPFVDKITWATGLDKDGRPIYNDASRPGAPGSEAKGSSVFVAPAFLGAKNWM 419
             G  I  F    K+     LD D       A+ PG    +     + ++     A   +
Sbjct: 151 LTGNPISEFGDGGKVDLRKNLDTDRDDFLIVANAPGVIFKDKIIIGMRLSEGLDAAPGHI 210

Query: 420 PMAYNKDTG----LFYV--PSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLR 473
             AYN  TG    +F+      E+G D W+     K G A   AG  +    E       
Sbjct: 211 -RAYNVKTGKREWIFHTIPQKGEFGYDTWDSEFIQKIGGANNWAGMVVDQKRE------- 262

Query: 474 AIDPISGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQ 528
            +   +G   +        WGG  T  G+ ++  +    L A +A TG+++W FQ
Sbjct: 263 IVFVPTGSATY------DFWGGYRT--GDNLYANS----LVALDANTGERIWHFQ 305



 Score = 32.3 bits (72), Expect = 7e-05
 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 3/50 (6%)

Query: 511 GFLQAFNAKTGDKVWEFQT--GSGVLGSPVTWEMDGEQYVSVVSGWGGAV 558
           G ++A+N KTG + W F T    G  G   TW+ +  Q +   + W G V
Sbjct: 208 GHIRAYNVKTGKREWIFHTIPQKGEFGYD-TWDSEFIQKIGGANNWAGMV 256



 Score = 32.3 bits (72), Expect = 7e-05
 Identities = 29/90 (32%), Positives = 37/90 (41%), Gaps = 2/90 (2%)

Query: 497 LTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGVLGSPVTWEMDG-EQYVSVVSGWG 555
           L TK  +  +  P G L A +  TG K W+   G     S   +E  G E Y   V   G
Sbjct: 575 LLTKDGVYGSNPPWGLLTAIDMNTGKKKWQVTLGEINSLSAQGFEPTGTENYGGPVVTAG 634

Query: 556 GAVPLWGGEVAK-RVKDFNQGGMLWTFKLP 584
           G + +   +  K R  D   G  LW  KLP
Sbjct: 635 GLLFIAATKDEKIRAFDKETGEKLWEAKLP 664



 Score = 30.8 bits (68), Expect = 2e-04
 Identities = 25/125 (20%), Positives = 46/125 (36%), Gaps = 29/125 (23%)

Query: 414 GAKNWMPMAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLR 473
           GA NW  M  ++   + +VP+     D W     Y+ G             +  Y   L 
Sbjct: 248 GANNWAGMVVDQKREIVFVPTGSATYDFWG---GYRTG-------------DNLYANSLV 291

Query: 474 AIDPISGKEVWRHKN-YAPLWGGVLTTKGNL------------VFTGTPEGFLQAFNAKT 520
           A+D  +G+ +W  +  +  +W        NL            V   + +G    F+ ++
Sbjct: 292 ALDANTGERIWHFQAVHHDVWDRDFPANPNLIRIQKEGEWIDAVAQISKQGMTYVFDRES 351

Query: 521 GDKVW 525
           G+ +W
Sbjct: 352 GEPIW 356



 Score = 26.2 bits (56), Expect = 0.005
 Identities = 29/107 (27%), Positives = 44/107 (41%), Gaps = 15/107 (14%)

Query: 155 LVALNKDTGKVVWSKKVADHKEGYSISAAPMIVNGKLITG----VAGGEFGVVG----KI 206
           L A++ +TGK  W   + +     S+SA      G    G     AGG   +      KI
Sbjct: 591 LTAIDMNTGKKKWQVTLGEIN---SLSAQGFEPTGTENYGGPVVTAGGLLFIAATKDEKI 647

Query: 207 QAYNPENGELLW-MRPTVEGHMG---YVYKDGKAIENGISGGEAGKT 249
           +A++ E GE LW  +    GH     Y Y   + +     GG+  K+
Sbjct: 648 RAFDKETGEKLWEAKLPAAGHATPAMYEYDGKQFLVIACGGGKGTKS 694


Lambda     K      H
   0.317    0.137    0.438 

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: 1557
Number of extensions: 133
Number of successful extensions: 18
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 8
Number of HSP's successfully gapped: 8
Length of query: 595
Length of database: 705
Length adjustment: 38
Effective length of query: 557
Effective length of database: 667
Effective search space:   371519
Effective search space used:   371519
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: 41 (21.6 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:

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