GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-large in Burkholderia phytofirmans PsJN

Align Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8 (characterized)
to candidate BPHYT_RS01765 BPHYT_RS01765 carbon-monoxide dehydrogenase

Query= SwissProt::Q4J6M3
         (748 letters)



>FitnessBrowser__BFirm:BPHYT_RS01765
          Length = 793

 Score =  466 bits (1200), Expect = e-135
 Identities = 287/789 (36%), Positives = 428/789 (54%), Gaps = 53/789 (6%)

Query: 5   GKSIKRLNDDKFITGRSNYIDDIKIPS-LYAGFVRSPYPHAIIKRIDATDALKVNGIVAV 63
           G S++R  D +F+TG   Y DDI +P   YA F+RSP+ HA I  ID   A +  G+VA+
Sbjct: 10  GASVERKEDYRFLTGNGQYTDDIVLPQQTYAIFLRSPHAHAKINSIDTAAAKQSPGVVAI 69

Query: 64  FSGKDINPMLKGGVGVLSAYVNPSLFRFKERKAFPED-------NKVKYVGEPVAIVIGQ 116
           F+G D   M    VG L       L    + K   E         KV++VG+ VA+VI  
Sbjct: 70  FTGAD---MAADNVGGLPC---GWLIHSTDGKPMNEPPHPIIAHTKVRHVGDQVALVIAD 123

Query: 117 DKYAVRDAIDRVNVEYEQLKPVIKMEDA-EKDEVIVHDELKTNVSYKIPFKAGD---IEK 172
              A +DA + + V+Y+ L  V+    A +  +  VHDE+  N+ Y   +  GD    + 
Sbjct: 124 SIKAAKDAAELIEVDYDVLPAVVDTAHAADAGQPAVHDEVPDNICYN--WGHGDKAATDA 181

Query: 173 AFSQADKVVKVEAINERLIPNPMEPRGILSVYD--GNSLSVWYSTQVPHFARSEFAR-IF 229
           AF++A  V  ++ +N RL+PN +EPR + + Y    +S +++ + Q PH  R   A  + 
Sbjct: 182 AFAKAAHVTTLDIVNNRLVPNAIEPRAVNASYSVQDDSYTLYVANQNPHVERLLMAAFVL 241

Query: 230 GIPETKIRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLA-SEARS 288
            +PE+K+RV  PDVGG FGSK+ + AE++A+  +S  +RRPV+WTA RSE  ++ +  R 
Sbjct: 242 SLPESKLRVIAPDVGGGFGSKIFLYAEDVALTWASKKIRRPVKWTAERSEAFVSDAHGRD 301

Query: 289 NVFTGEVAVKKDGTVLGIKGKLLLDLGAYLTLTAGIQPTII-PVMIPGPYKVRDLEIEST 347
           +V   E+A+  DG  LG++     ++GAYL+  A   PTI+   ++ G Y    +  E  
Sbjct: 302 HVTKAELAMDADGKFLGMRIHTTANMGAYLSTFASSVPTILYATLLAGQYATPAIYAEVK 361

Query: 348 AVYTTTPPITMYRGASRPEATYIIERIMSTVADELGLDDVTIRERNLIDQLPYTNPFGLR 407
           AV+T T P+  YRGA RPEATY++ER++ T A ++ LD   IR RN I + PY  P GL 
Sbjct: 362 AVFTNTVPVDAYRGAGRPEATYVVERLVETAARDMKLDPAEIRRRNFIREFPYATPVGLT 421

Query: 408 YDTGDYIRVFKDGVAKLEYNELRKWAQQERSKGHRVGVGLAFYLEICSFGP--------- 458
           YDTGDY  +    +   +        Q+    G   G+G + Y+E C   P         
Sbjct: 422 YDTGDYETILARSLELADVKGFAARKQESEKNGKLRGLGYSCYIEACGLAPSNIAGALGA 481

Query: 459 ----WEYGEIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPIEKIRVVWGDTDIV 514
               +E G+I+V   G+V V TG+  HGQG ET  AQ+VAD L I +E + +V GDT  +
Sbjct: 482 RAGLFEVGQIRVHPTGSVTVFTGSHSHGQGHETTFAQVVADRLGIALESVEIVHGDTGRI 541

Query: 515 EGSFGTYGSRSLTIGGSAALKVAERVLDKMKRAAASYFNADVQEIRYENEEFSVKNDPSK 574
               GTYGSRS+ +GGSA +K  +++  K K+ AA    A  ++I +++  F V      
Sbjct: 542 PFGMGTYGSRSIAVGGSAIMKALDKIETKAKKIAAHLLEAAAEDIEFKDGVFRVAGTDRT 601

Query: 575 KASWD-EIASLATTKEP-------IVEKIYYE-NDVTFPYGVHVAVVEVD-DLGMARVVE 624
           KA  D  +A+      P       + E  +Y+  + T+P G ++  +EVD + G+ R+ +
Sbjct: 602 KAFADISLAAYVPHNYPLDVLEPGLEESAFYDPTNFTYPSGAYICEIEVDPETGVCRIQQ 661

Query: 625 YRAYDDIGKVINPALAEAQIHGGGVQGVGQALYEKAII-NENGQ-LSVTYADYYVPTAVE 682
           + A DD G VINP + E Q+HGG  QG+GQA+ E+ +  NE+GQ LS +Y DY +P A +
Sbjct: 662 FTAVDDFGNVINPMIVEGQVHGGLAQGIGQAMLERCVYDNESGQLLSGSYMDYAMPHASD 721

Query: 683 APRFISYFADKSHPSNYPTGTKGVGEAALIVGPAAIIRAIEDA---VGARFTKTPTPPEE 739
            P F       +  ++ P G KG GEA  I  P A+I AI DA   +G    + P  P  
Sbjct: 722 LPNFTVETVKGTPCTHNPLGVKGCGEAGAIGSPPAVINAILDALAPLGVTDLQMPATPHR 781

Query: 740 IYKAIMSKK 748
           ++ AI + K
Sbjct: 782 VWSAIHAAK 790


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: 1380
Number of extensions: 62
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: 748
Length of database: 793
Length adjustment: 41
Effective length of query: 707
Effective length of database: 752
Effective search space:   531664
Effective search space used:   531664
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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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:

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:

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:

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:

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