GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-large in Pandoraea thiooxydans ATSB16

Align Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8 (characterized)
to candidate WP_047216151.1 PATSB16_RS01635 xanthine dehydrogenase family protein molybdopterin-binding subunit

Query= SwissProt::Q4J6M3
         (748 letters)



>NCBI__GCF_001931675.1:WP_047216151.1
          Length = 790

 Score =  456 bits (1174), Expect = e-132
 Identities = 287/780 (36%), Positives = 424/780 (54%), Gaps = 43/780 (5%)

Query: 5   GKSIKRLNDDKFITGRSNYIDDIKIPS-LYAGFVRSPYPHAIIKRIDATDALKVNGIVAV 63
           G++++R  D +F+TG   Y DD+++    YA FVRSPY HA I+      A +  G+V +
Sbjct: 10  GQAVRRKEDYRFLTGAGQYTDDVQMDGQTYAYFVRSPYAHARIRGYRLDAARQAPGVVGI 69

Query: 64  FSGKDINPMLKGGV--GVLSAYVNPSLFRFKERKAFPEDNKVKYVGEPVAIVIGQDKYAV 121
           F+G+DI     GG+  G L   V+    +         D  V+YVG+ VA+VI Q     
Sbjct: 70  FTGEDIKRAGIGGLPCGWLITDVHGQPMKEPPHPVLAIDT-VRYVGDQVALVIAQTLAQA 128

Query: 122 RDAIDRVNVEYEQLKPVIKMEDAEKDEV-IVHDELKTNVSYKIPFKAGD---IEKAFSQA 177
           RDA + V+V+YE L  V+  + A +     VHD    NV Y   +  GD   ++ A ++A
Sbjct: 129 RDAAELVDVDYEPLDAVVAPDAAVRSGAPAVHDIAPDNVCYV--WSLGDQAAVDAAMAKA 186

Query: 178 DKVVKVEAINERLIPNPMEPRGILSVYD--GNSLSVWYSTQVPHFARSEFAR-IFGIPET 234
             V +++ +N RLIPN +EPR  ++ Y    +S +++ + Q PH  R   A  +  +PE 
Sbjct: 187 AHVTRLDFVNNRLIPNAIEPRAAVAHYSRADDSYTLYVANQNPHVERLLMAAFVLNLPEH 246

Query: 235 KIRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLA-SEARSNVFTG 293
           K+RV  PDVGG FGSK+ + AEE A++ +S  + RP++WTA RSE  L+ +  R +V T 
Sbjct: 247 KLRVVAPDVGGGFGSKIFLYAEETALVWASKQINRPIKWTAERSESFLSDAHGRDHVTTA 306

Query: 294 EVAVKKDGTVLGIKGKLLLDLGAYLTLTAGIQPTII-PVMIPGPYKVRDLEIESTAVYTT 352
           E+ +  +G  L ++     +LGAYL+  A   PTI+   ++ G Y    +  E T V+T 
Sbjct: 307 ELGLDANGKFLALRVHTKANLGAYLSTFASSVPTILYATLLAGQYTTPAIFCEVTGVFTH 366

Query: 353 TPPITMYRGASRPEATYIIERIMSTVADELGLDDVTIRERNLIDQLPYTNPFGLRYDTGD 412
           T P+  YRGA RPEATY++ERI+ T A E+ +D V +R RN I Q PY  P  L YDTG+
Sbjct: 367 TAPVDAYRGAGRPEATYVVERIVETAAREMKIDPVELRRRNFITQFPYQTPVALCYDTGN 426

Query: 413 YIRVFKDGVAKLEYNELRKWAQQERSKGHRVGVGLAFYLEICSFGP-------------W 459
           Y       +   +        +  R +G   G+G + Y+E C   P             +
Sbjct: 427 YGASLDKALQLADVAGFPARREAARQRGKLRGLGYSCYIEACGLAPSNIAGQLGARAGLF 486

Query: 460 EYGEIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPIEKIRVVWGDTDIVEGSFG 519
           E GE++V   G V V TG+  HGQG ET   QIVAD L I  E + +V GDT  V    G
Sbjct: 487 EAGEVRVHPTGKVTVFTGSHSHGQGHETTFTQIVADRLGIAYEDVDIVHGDTGRVPFGMG 546

Query: 520 TYGSRSLTIGGSAALKVAERVLDKMKRAAASYFNADVQEIRYENEEFSVKNDPSKKASWD 579
           TYGSRSL +GGSA +K  ++V+ K K+ AA    A   +I +++ +FSV     K   + 
Sbjct: 547 TYGSRSLAVGGSAIVKALDKVIAKGKKIAAHMLEAAEGDIEFKDGKFSVAG-TDKALPFA 605

Query: 580 EIA---------SLATTKEPIVEKIYYE-NDVTFPYGVHVAVVEVD-DLGMARVVEYRAY 628
           +IA          L + +  + E  +Y+  + T+P G H+  VEVD D G   +V   A 
Sbjct: 606 QIALSAYVPHNYPLESLEPGLDESAFYDPTNFTYPAGSHICEVEVDPDTGQTEIVAMTAV 665

Query: 629 DDIGKVINPALAEAQIHGGGVQGVGQALYEKAIIN-ENGQ-LSVTYADYYVPTAVEAPRF 686
           DD G ++NP + E Q+HGG  QG+GQAL E  + + E+GQ L+ +Y DY +P A + P F
Sbjct: 666 DDFGNIVNPMIVEGQVHGGLAQGIGQALLEGCVYDPESGQLLTGSYMDYAMPRADDLPSF 725

Query: 687 ISYFADKSHPSNYPTGTKGVGEAALIVGPAAIIRAIEDAVGARFTKTPTPPEEIYKAIMS 746
            +     +  ++ P G KG GEA  I  P A+I AI DA+G    + P  PE +++A+ +
Sbjct: 726 -AVDTTCTPCTHNPLGVKGCGEAGAIGSPPAVINAITDALGVLHLEMPATPERVWRALQT 784


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: 1409
Number of extensions: 72
Number of successful extensions: 14
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: 790
Length adjustment: 41
Effective length of query: 707
Effective length of database: 749
Effective search space:   529543
Effective search space used:   529543
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 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:

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