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 Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8 (characterized)
to candidate H281DRAFT_02182 H281DRAFT_02182 xanthine dehydrogenase, molybdenum binding subunit apoprotein

Query= SwissProt::Q4J6M3
         (748 letters)



>FitnessBrowser__Burk376:H281DRAFT_02182
          Length = 795

 Score =  476 bits (1224), Expect = e-138
 Identities = 294/790 (37%), Positives = 433/790 (54%), Gaps = 55/790 (6%)

Query: 5   GKSIKRLNDDKFITGRSNYIDDIKIPS-LYAGFVRSPYPHAIIKRIDATDALKVNGIVAV 63
           G S++R  D +F+TG   Y DDI +P   YA F+RSP+ HA I  ID T A +  G+VA+
Sbjct: 11  GASVERKEDYRFLTGNGQYTDDILLPQQTYAVFLRSPHAHAKINSIDTTAAKQSPGVVAI 70

Query: 64  FSGKDINPMLKGGVGVLSAYVNPSLFRFKERKAFPED-------NKVKYVGEPVAIVIGQ 116
           F+G D+     GG+          L    + K   E         KV++VG+ VA+VI  
Sbjct: 71  FTGADMAAENVGGLPC------GWLIHSTDGKPMNEPPHPIIAHTKVRHVGDQVALVIAD 124

Query: 117 DKYAVRDAIDRVNVEYEQLKPVIKMEDA-EKDEVIVHDELKTNVSYKIPFKAGD---IEK 172
              A +DA + + V+Y+ L  V+    A +  +  VHDE+  NV Y   +  GD    + 
Sbjct: 125 SIKAAKDAAELIEVDYDVLPAVVDTAHAADAGQPAVHDEVPDNVCYN--WGHGDKAATDA 182

Query: 173 AFSQADKVVKVEAINERLIPNPMEPRGILSVYDG--NSLSVWYSTQVPHFARSEFAR-IF 229
           AF++A  V  ++ +N RL+PN +EPR + + Y    +S +++ + Q PH  R   A  + 
Sbjct: 183 AFAKAAHVTTLDIVNNRLVPNAIEPRAVNASYSSQDDSYTLYVANQNPHVERLLMAAFVL 242

Query: 230 GIPETKIRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLA-SEARS 288
            +PE+K+RV  PDVGG FGSK+ + AE++A+  +S  +RRPV+WTA RSE  L+ +  R 
Sbjct: 243 SLPESKLRVIAPDVGGGFGSKIFLYAEDVALTWASKKIRRPVKWTAERSEAFLSDAHGRD 302

Query: 289 NVFTGEVAVKKDGTVLGIKGKLLLDLGAYLTLTAGIQPTII-PVMIPGPYKVRDLEIEST 347
           +V   E+A+  DG  L ++   + ++GAYL+  A   PTI+   ++ G Y    +  E  
Sbjct: 303 HVTKAELAMDADGKFLAMRIHTIANMGAYLSTFASSVPTILYATLLAGQYATPAIYAEVK 362

Query: 348 AVYTTTPPITMYRGASRPEATYIIERIMSTVADELGLDDVTIRERNLIDQLPYTNPFGLR 407
           AV+T T P+  YRGA RPEATY++ER++ T A E+ LD   IR RN I + PY  P GL 
Sbjct: 363 AVFTNTVPVDAYRGAGRPEATYVVERLVETAAREMKLDPAEIRRRNFIREFPYATPVGLT 422

Query: 408 YDTGDYIRVFKDGVAKLEYNELRKWAQQERSKGHRVGVGLAFYLEICSFGP--------- 458
           YDTGDY  +    +   +        Q+    G R G+G + Y+E C   P         
Sbjct: 423 YDTGDYETILARSLELADVKGFEARRQESERNGKRRGLGYSCYIEACGLAPSNIAGALGA 482

Query: 459 ----WEYGEIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPIEKIRVVWGDTDIV 514
               +E G+I+V   G+V V TG+  HGQG ET  AQ+VAD L +P+E + +V GDT  +
Sbjct: 483 RAGLFEVGQIRVHPTGSVTVFTGSHSHGQGHETTFAQVVADRLGLPLESVEIVHGDTGRI 542

Query: 515 EGSFGTYGSRSLTIGGSAALKVAERVLDKMKRAAASYFNADVQEIRYENEEFSVKNDPSK 574
               GTYGSRS+ +GGSA +K  +++  K K+ AA    A  ++I +++  F V      
Sbjct: 543 PFGMGTYGSRSIAVGGSAIMKALDKIETKAKKIAAHLLEAATEDIEFKDGVFRVAGTDRT 602

Query: 575 KASWDEIASLA--------TTKEPIVEK--IYYENDVTFPYGVHVAVVEVD-DLGMARVV 623
           KA + EI+  A           EP +E+   Y  ++ T+P G ++  VEVD D G+ R+ 
Sbjct: 603 KA-FAEISLAAYVPHNYPLDVLEPGLEESAFYDPSNFTYPSGAYICEVEVDPDTGVCRIQ 661

Query: 624 EYRAYDDIGKVINPALAEAQIHGGGVQGVGQALYEKAII-NENGQ-LSVTYADYYVPTAV 681
            + A DD G VINP + E Q+HGG  QG+GQA+ E+ +  NE+GQ LS +Y DY +P A 
Sbjct: 662 RFTAVDDFGNVINPMIVEGQVHGGLGQGIGQAMLERCVYDNESGQLLSGSYMDYAMPHAS 721

Query: 682 EAPRFISYFADKSHPSNYPTGTKGVGEAALIVGPAAIIRAIEDA---VGARFTKTPTPPE 738
           + P F    A  +  ++ P G KG GEA  I  P A+I AI DA   +G    + P  P 
Sbjct: 722 DLPDFTVETAKGTPCTHNPLGVKGCGEAGAIGSPPAVINAIIDALAPLGVTDLQMPATPH 781

Query: 739 EIYKAIMSKK 748
            ++ AI + K
Sbjct: 782 RVWSAIHAVK 791


Lambda     K      H
   0.317    0.136    0.390 

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: 1368
Number of extensions: 66
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: 748
Length of database: 795
Length adjustment: 41
Effective length of query: 707
Effective length of database: 754
Effective search space:   533078
Effective search space used:   533078
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: 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