GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Novosphingobium fuchskuhlense FNE08-7

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_067913032.1 AQZ52_RS15535 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase

Query= reanno::Smeli:SMc02322
         (699 letters)



>NCBI__GCF_001519075.1:WP_067913032.1
          Length = 702

 Score =  831 bits (2147), Expect = 0.0
 Identities = 425/690 (61%), Positives = 510/690 (73%), Gaps = 11/690 (1%)

Query: 14  WDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWVKGSG 73
           WDD  AA ++  E LLYRSNLLGSD  +TN+GGGNTSAK+   DPLTGE V VLWVKGSG
Sbjct: 20  WDDAHAASLSPAELLLYRSNLLGSDLTVTNFGGGNTSAKLTGIDPLTGEAVPVLWVKGSG 79

Query: 74  GDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTPLHAY 133
           GD+G++K+DGFSTLY +KL  L+  Y G + +D MVGYLPHCTFNLN RAASIDTPLH+ 
Sbjct: 80  GDIGSMKLDGFSTLYQEKLLGLEAHYSGPDDDDTMVGYLPHCTFNLNGRAASIDTPLHSL 139

Query: 134 VPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQENPD 193
           +P  HVDH+HPDAIIA+AAS      T  I+G  IGWLPWKRPGY LG+ L  + + NP 
Sbjct: 140 LPFAHVDHVHPDAIIALAASSGGEAATRAIWGGTIGWLPWKRPGYTLGVMLRDYVRANPQ 199

Query: 194 ARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTG-PAFGGRSKPVLAAADRA 252
            +GV+L  HG+  W D+AK  YE TI +I  A         G PAFGG+   V    DRA
Sbjct: 200 VKGVMLAGHGIICWADSAKACYEHTISLIADAARHLNAAMAGKPAFGGQI--VAPNPDRA 257

Query: 253 AIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRTKIRP 312
           AIA  LMP +RGL++    K+GHF D    L+F  S   + LAALGTSCPDHFLRTKI P
Sbjct: 258 AIAADLMPRLRGLMTGARRKLGHFSDDAEALEFTGSADFQRLAALGTSCPDHFLRTKIAP 317

Query: 313 LVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDPNAVVYLVPGVGM 372
           L +D      D     A L + +A YRA YAAYYERCKRA+SPAMRDPN VV LVPGVG 
Sbjct: 318 LTLDPARLTDD-----AYLAQQLADYRALYAAYYERCKRANSPAMRDPNPVVVLVPGVGR 372

Query: 373 ITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEAKLQRMPKP 432
           ITFA DK TAR++ EFY NAINVMRGA  +  Y+ L EQEAFDIEYWLLEEAKLQRMP P
Sbjct: 373 ITFATDKTTARLAGEFYGNAINVMRGAEAIGDYIALDEQEAFDIEYWLLEEAKLQRMPAP 432

Query: 433 KSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTRYGKDFVRS 492
           K + GRIALVTGGAGGIG ATA RL++EGACV+LAD D  ALE  +  L+ ++GKD +R+
Sbjct: 433 KPMVGRIALVTGGAGGIGAATAVRLLKEGACVLLADRDADALEETRAGLAQQFGKDVIRA 492

Query: 493 VNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNMDILATGYF 552
              +VT EAAV + F      FGGLD+LV+NAG+A+SA +E+TTL+LW++N D+LA GYF
Sbjct: 493 ATCDVTDEAAVAAAFAACAREFGGLDMLVANAGIASSATIEETTLSLWHRNHDVLAQGYF 552

Query: 553 LVSREAFRIFRNQK--AGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLALEGASA 610
           L +R A+ + +  K   G +VVF+ SKN LAA+ GASAY +AKAA  HLARCLALEGA  
Sbjct: 553 LTARAAWPLLKRMKEQGGTSVVFIGSKNALAAAAGASAYASAKAAANHLARCLALEGAPD 612

Query: 611 QIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDV-DELEAHYRERSMLKLSVFPEDIAE 669
            IRVN+VNPDAV+RGS+IW G+W+++RAAA K+D  +ELEAHYR RSMLK  V PEDIAE
Sbjct: 613 GIRVNIVNPDAVIRGSRIWDGDWRKERAAANKVDAGEELEAHYRNRSMLKRDVLPEDIAE 672

Query: 670 AIYFLASDMSAKSTGNIVNVDAGNAQSFTR 699
           A  +LASD+SAKSTGN++NVDAGN Q+FTR
Sbjct: 673 AAAWLASDLSAKSTGNMINVDAGNVQAFTR 702


Lambda     K      H
   0.317    0.133    0.393 

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: 1233
Number of extensions: 52
Number of successful extensions: 5
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: 699
Length of database: 702
Length adjustment: 39
Effective length of query: 660
Effective length of database: 663
Effective search space:   437580
Effective search space used:   437580
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: 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:

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