Alignments for a candidate for nbaE in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for nbaE in Sinorhizobium medicae WSM419

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_012061562.1 SMED_RS23160 aldehyde dehydrogenase family protein

Query= BRENDA::Q83XU8
         (485 letters)



>NCBI__GCF_000017145.1:WP_012061562.1
          Length = 794

 Score =  308 bits (790), Expect = 3e-88
 Identities = 176/444 (39%), Positives = 249/444 (56%), Gaps = 22/444 (4%)

Query: 25  PLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDFL 84
           P   A++A +   GR +VDAAVAAA+ A +G W ++S   R   LYA+A  I R      
Sbjct: 55  PATGALLAGIARGGREDVDAAVAAARKA-QGPWAKLSGHARARHLYALARLIQRHARLIA 113

Query: 85  AAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRPV 144
             E  D GKP+   R +D+P  A +F   A   +   TEF              A + PV
Sbjct: 114 VVEALDNGKPIRETRDIDVPLAARHFYHHAGWAQLQETEF--------------ADQVPV 159

Query: 145 GVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVYN 204
           GVVG + PWN P L++ WKV PALA GNTV++KP+E TP TA L  E+   +G+PPGV N
Sbjct: 160 GVVGQVIPWNFPFLMLAWKVAPALALGNTVILKPAEYTPLTALLFAEMAAASGLPPGVLN 219

Query: 205 VVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVFA 264
           VV G G   TG  +  H D++ I FTG T  G  I +  A   + ++LELGGK+  IVF 
Sbjct: 220 VVTGEG--ETGALIVEHEDIDKIAFTGSTEIGRLIREKTAGSGKSLTLELGGKSPFIVFD 277

Query: 265 DCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLAT 324
           D D+D A+EG + + + N GQVC    R+ V+  +   F  RLK+  + +++G P D + 
Sbjct: 278 DADIDAAVEGVVDAIWFNQGQVCCAGSRLLVQEGVAPVFHERLKRRMDTLRVGHPLDKSI 337

Query: 325 GMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDSV 384
            M  +++    +++     K V  GA++      P + E  KGG++ +PT+ TG+   SV
Sbjct: 338 DMAAIVAPVQLQRIAELVAKGVAEGASMHQ----PRI-ELPKGGSFYRPTLLTGVQPTSV 392

Query: 385 VAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWVN 444
           VA EEIFGP A+ M F + +E I+ AN + YGLA  +W+  +  A  VA  +  G+ WVN
Sbjct: 393 VATEEIFGPVAVSMTFRTPDEAIQLANHSRYGLAASVWSETIGLALHVAAKLAAGVVWVN 452

Query: 445 SWFLRDLRTAFGGSKQSGIGREGG 468
           +  L D    FGG ++SG GREGG
Sbjct: 453 ATNLFDAAAGFGGKRESGFGREGG 476



 Score = 90.1 bits (222), Expect = 3e-22
 Identities = 66/201 (32%), Positives = 97/201 (48%), Gaps = 14/201 (6%)

Query: 30  VIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDFLAAEVE 89
           V+ +V E  R ++  AV AA+ A    W   +   R ++LY +A+ ++ R  +F      
Sbjct: 545 VVGEVGEGNRKDIRNAVVAARGA--SGWSSATAHNRAQILYYIAENLSSRGAEFADRIAA 602

Query: 90  DTGKPMSLARHVDIPRGAA---NFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRPVGV 146
            TG   + AR  ++    A   ++  +AD  + V       P   GV     A+  P GV
Sbjct: 603 MTGASAASAR-TEVEASIARLFSYGAWADKYEGV----VHQPPLRGVAL---AMPEPQGV 654

Query: 147 VGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVYNVV 206
           VGVICP   PLL +   V P +A GN V+  PSE  P  A     V+ T+ VPPGV N+V
Sbjct: 655 VGVICPPEAPLLGLVSLVAPLIAVGNRVIAVPSETHPLAATDFYSVLETSDVPPGVINIV 714

Query: 207 HGFGPNSTGEFLTSHPDVNAI 227
            G       + L +H DV+A+
Sbjct: 715 TGLA-TELAKALAAHNDVDAL 734


Lambda     K      H
   0.318    0.135    0.406 

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: 924
Number of extensions: 48
Number of successful extensions: 5
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: 485
Length of database: 794
Length adjustment: 37
Effective length of query: 448
Effective length of database: 757
Effective search space:   339136
Effective search space used:   339136
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 Apr 09 2024. 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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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