GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Sinorhizobium meliloti 1021

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate SM_b21301 SM_b21301 ly membrane-anchored aldehyde dehydrogenase

Query= BRENDA::Q1XGK8
         (486 letters)



>FitnessBrowser__Smeli:SM_b21301
          Length = 794

 Score =  330 bits (847), Expect = 8e-95
 Identities = 192/467 (41%), Positives = 267/467 (57%), Gaps = 22/467 (4%)

Query: 3   EIKHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLS 62
           ++ HFINGAFVGSASG++F+   P+ G+++  +   GR +V+AAV AAR A +GPW KLS
Sbjct: 32  KLGHFINGAFVGSASGKSFDTFEPATGKLLAKIAHGGRDDVNAAVAAARKA-QGPWAKLS 90

Query: 63  VAERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVA 122
              RA  L+ +A  I          E LD GKP      IDIP  A +F   A   +   
Sbjct: 91  GHARARHLYALARLIQRHARLIAVVEALDNGKPIRETRDIDIPLAARHFYHHAGWAQLQE 150

Query: 123 NEAFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEE 182
            E              +A + P GV+G + PWN P L++ WKV PALA GN+V++KP+E 
Sbjct: 151 TE--------------FADQVPVGVVGQVIPWNFPFLMLAWKVAPALALGNSVILKPAEF 196

Query: 183 TPLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMR 242
           TPLTA L  E+  AAG+P GV NVV G G    GA + EH D+D   FTG T  G +I  
Sbjct: 197 TPLTALLFAELAAAAGLPPGVLNVVTGEG--ETGALIVEHEDIDKIAFTGSTEVGRLIRE 254

Query: 243 AAAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFD 302
             A   + ++LELGGK+  IVF D D+D A+EG + + + N GQVC    R+ V+  +  
Sbjct: 255 KTAGSGKSLTLELGGKSPFIVFDDADIDAAVEGVVDAIWFNQGQVCCAGSRLLVQEGVAP 314

Query: 303 EFVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDM 362
            F  RLK   E+L +G P D + +   +V+    +++     + V +G S+       ++
Sbjct: 315 VFHDRLKRRMETLRVGHPLDKAIDMAAIVAPVQLQRIEELVAKGVAEGASMHQPK--IEL 372

Query: 363 PAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAI 422
           P    GG++ +PT+ TG+   S V TEEIFGP      F T EEAI+LAN   YGLA+++
Sbjct: 373 PK---GGSFFRPTLLTGVQPTSVVATEEIFGPVAVSMTFRTPEEAIQLANHSRYGLAASV 429

Query: 423 WTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGG 469
           W+E    A  VA ++ AG+VWVN+  L D  + FGG ++SG GREGG
Sbjct: 430 WSETIGLALHVAAKLAAGVVWVNATNLFDASSGFGGKRESGFGREGG 476



 Score = 95.9 bits (237), Expect = 5e-24
 Identities = 80/255 (31%), Positives = 121/255 (47%), Gaps = 28/255 (10%)

Query: 29  GQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVAERAEILHRVADGITARFDEFLEAE 88
           G+VIG V E  R ++  AV AAR A    W   +   RA+IL+ +A+ +++R  EF    
Sbjct: 543 GKVIGEVGEGNRKDIRNAVVAARGA--SGWSSATAHNRAQILYYIAENLSSRGAEFAGRI 600

Query: 89  CLDTGKPKSLASHIDIPRGAA---NFKVFADLLKNVANEAFEMATPDGAGAINYAVRRPK 145
              TG   + A   ++    A   ++  +AD  +   ++      P   G +  A+  P+
Sbjct: 601 AAMTGASAANA-RAEVEASIARLFSYGAWADKYEGTVHQ------PPLRG-VALAMPEPQ 652

Query: 146 GVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPLTATLLGEVMQAAGVPAGVYN 205
           GV+GVI P   PLL +   V P +A GN VV  PSE  PL AT    V++ + VP GV N
Sbjct: 653 GVVGVICPPEAPLLGLVSLVAPLIAVGNRVVAVPSEAHPLAATDFYSVLETSDVPPGVIN 712

Query: 206 VVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAAAKGVRQVSLELGGKNAGIVFA 265
           +V G   + A A L  H DVDA    G      ++ + +   +++  ++ G         
Sbjct: 713 IVTGSAIELAKA-LAAHNDVDALWAFGSPELSTLVEKLSVGNLKRTFVDYG--------- 762

Query: 266 DCDMDKAIEGTLRSA 280
                KAI+ T RSA
Sbjct: 763 -----KAIDWTDRSA 772


Lambda     K      H
   0.318    0.136    0.411 

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: 1045
Number of extensions: 50
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 486
Length of database: 794
Length adjustment: 37
Effective length of query: 449
Effective length of database: 757
Effective search space:   339893
Effective search space used:   339893
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: 53 (25.0 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