Alignments for a candidate for aldox-large in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Paraburkholderia bryophila 376MFSha3.1

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate H281DRAFT_02676 H281DRAFT_02676 xanthine dehydrogenase, molybdenum binding subunit apoprotein (EC 1.17.1.4)

Query= metacyc::MONOMER-18071
         (749 letters)



>FitnessBrowser__Burk376:H281DRAFT_02676
          Length = 788

 Score =  390 bits (1003), Expect = e-112
 Identities = 247/771 (32%), Positives = 393/771 (50%), Gaps = 33/771 (4%)

Query: 3   YVGKPVKRIYDDKFVTGRSTYVDDIRIP-ALYAGFVRSTYPHAIIKRIDVSDALKVNGIV 61
           Y+GK V R  D K + G+ +YVDD+ +P  L A  +RS++ HA I  ID + A ++ G+ 
Sbjct: 15  YIGKRVTRTEDKKLLQGQGSYVDDVHLPNMLQAAVLRSSHAHAKIVSIDCTAARELKGVH 74

Query: 62  AVFTAKEINPLLKGGIRPWPTYIDIRSFRYSE-RKAFPENKVKYVGEPVAIVLGQDKYSV 120
           AV+T  +++   +G     P+ +   + R+   ++     +V + GE VA V+  ++Y  
Sbjct: 75  AVYTHADLSGRARGRA---PSMLPNPAIRFERTQELLASTEVTFAGEAVAFVVADNRYIA 131

Query: 121 RDAIDKVVVEYEPLKPVIRMEEAEK-DQVIIHEELKTNISYKIPFKAGEVDKAFSESDKV 179
            DA   + VEY+ L  V    +  + +  + H + K N+   I    G++D AF+ +  V
Sbjct: 132 EDACGLIEVEYDTLPAVADCRDGLRPESPLCHTDAKDNVVAHIEMGFGDIDAAFNGAPHV 191

Query: 180 VRVEAINERLIPNPMEPRGIVSRFEA--GTLSIWYSTQVPHYMRSEFARILGIPESKIKV 237
           V       R   +PME RG ++ F A  G L++W S Q PH+ +     +L     K++V
Sbjct: 192 VEETYWQNRGSAHPMETRGYLAEFHAANGELTVWSSGQAPHHEKKNLVELLEWDAEKLRV 251

Query: 238 SMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNVFTGEVAV 296
            M DVGG FG K+   PEE  V  +++ L RPV+W   R E  LA ++ R   +T ++A+
Sbjct: 252 LMNDVGGGFGPKLPFYPEEALVAIAAVALKRPVKWIEDRREHFLAVTQERDQWWTVKIAL 311

Query: 297 KRDGTILGIKGKLLLDLGAYITVTAGIQPLIIPMMIPGPYKIRNLDIESVAVYTNTPPIT 356
           + DG I G+K +++ D GA++     I P I     PGPY I  +  +   VYTN    +
Sbjct: 312 ENDGKIRGVKLEMVHDNGAFLPWGI-ITPYISITTTPGPYVIPAMGAKLDVVYTNKCATS 370

Query: 357 MYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVT--ELPYTNPF------GLRYD 408
             RGA RP+A + +ERI+   A  LG+D   +R +NL+   ++PY   F       LRYD
Sbjct: 371 PVRGAGRPQAVFAMERILDKAARALGMDRAELRWRNLIQPEQMPYDAGFIYRDGSPLRYD 430

Query: 409 SGDYVGLLREGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGPWEYAEVRVDER 468
           SGDY    +  ++R  Y    +   E R++G  +G+G+A ++E    GP+E A VRV   
Sbjct: 431 SGDYPACQKAALERAKYSSFAQRKAEARREGRFIGIGMASFVEGTGMGPFEGATVRVQAN 490

Query: 469 GDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAASMGTYGSRSVTIG 528
           G + V+TG +P GQG +T  AQI A+ L + +  + VI GDT  ++  +GT+ SR     
Sbjct: 491 GRIAVITGASPQGQGHKTTFAQICAEQLNVPLETIDVITGDTGGISMGVGTFASRVTVNA 550

Query: 529 GSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMSWDDVASIAY--- 585
           G++    A+ + +KM  + A  W    +E+   +G    +    ++MS+  +A I+    
Sbjct: 551 GNSVYIAAQAVGEKMLTLTAHLWKCKPEELLLVEGHVARRAGIEQRMSYGQLAKISQGMP 610

Query: 586 -----RSHDPGLVE-KIIYENDVTFPYGVHIATVEVD-DTGVARVLEYRAYDDIGKVVNP 638
                     GL E K       T+  G  +  +EVD +TG   +L Y    D GK++NP
Sbjct: 611 GFTMPEGLTAGLEETKYFSPAQSTYCNGTAVVELEVDRETGHITILNYVMAHDSGKLINP 670

Query: 639 ALAEAQIHGGGVQAVGQALYEQALLNENGQLIVT-YADYYVPTAVEAPKFTSVFADQYHP 697
            + + Q+ G     +G A  E    +EN Q I T + +Y +P A + P    V  +   P
Sbjct: 671 MIVDGQVIGSVAHGIGNATLEWMQYDENAQPITTNFGEYLLPMATDVPNIDIVHLETPSP 730

Query: 698 SNYPTGSKGVGEAALIVGPAVIIRALEDAI---GTRFTKTPTTPEEILRAI 745
            N P G KG GE   I   A I+ A+EDA+   G  FT+ P  P+ + + +
Sbjct: 731 LN-PLGVKGAGEGGTIPAAAAIVAAIEDALSEYGVEFTEAPLVPQRVFQKL 780


Lambda     K      H
   0.317    0.136    0.394 

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: 1394
Number of extensions: 80
Number of successful extensions: 10
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: 749
Length of database: 788
Length adjustment: 41
Effective length of query: 708
Effective length of database: 747
Effective search space:   528876
Effective search space used:   528876
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 (21.7 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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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