Aligments for a candidate for praB in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments 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:

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, or view the source code.

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