GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Corynebacterium deserti GIMN1.010

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_082353398.1 CDES_RS06155 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_001277995.1:WP_082353398.1
          Length = 513

 Score =  208 bits (529), Expect = 4e-58
 Identities = 148/483 (30%), Positives = 233/483 (48%), Gaps = 14/483 (2%)

Query: 38  PLIINGER-VTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEE 96
           P IING   V  E + + +NPA    +  S+  A       A+ +A      WR      
Sbjct: 25  PHIINGHPLVEGERRGEVFNPAT-GAVTASLPFATTATVNAAVSAAQAVAPAWRATGLAR 83

Query: 97  RANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKE 156
           RA ++ K   II  RK E +A +  E GK   +A  + A  ++ +E+ A  +  +     
Sbjct: 84  RAAVMFKLHEIITSRKDELAALITEEQGKVLSDAAGEIARGLENVEFCAGLVHHMKGEFL 143

Query: 157 ILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAK 216
             +  G        P+GV   I+P+NF   + +      I  GNTVVLKP+   P     
Sbjct: 144 EQAAAGLDVHQVRQPLGVVACITPFNFPAMVPLWMITTAIAAGNTVVLKPSEKDPSAVNW 203

Query: 217 FVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPG 276
            VE   +AGLP+GV+N + G   E  + L+D P+   ++F GS  +   +Y RA  +   
Sbjct: 204 IVEAFHEAGLPEGVLNLIHGD-REAVEALIDDPRVQAVSFVGSTPIAQSIYTRATALG-- 260

Query: 277 QNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEV 336
               KRV    G K+ +VV  DADLD AA++ + + +G +G++C A S  V   D+ D++
Sbjct: 261 ----KRVQALGGAKNHMVVMPDADLDAAADAAVSAGYGAAGERCMAISVVVPVGDIADDL 316

Query: 337 LEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGR--LMTGGEGD-SS 393
           + K  +   +LT+G+ T+ D+ MGPVI   A E+I   I      G   ++ G   D   
Sbjct: 317 IAKISSRITDLTIGEGTDPDSEMGPVITSAAKERIEGLIAGSSDSGAEVVVDGRSVDLPD 376

Query: 394 TGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNR 453
            GFFI PT+I  + P   +  EEIFGPV++ ++   FD A+E+ N+ +Y    A+ TR+ 
Sbjct: 377 EGFFIGPTLIDHVKPGMPVYDEEIFGPVLSVARVGHFDEAVELINSCQYANGTAIFTRDG 436

Query: 454 AHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMS-GTDSKAGGPDYLALHMQAKTVS 512
               + +    VG +  N       +G   FGG+K S   D+   GP+    + + K V+
Sbjct: 437 RTAREFEFAIEVGMVGINVPIP-VPIGAFSFGGWKKSLFGDTHMYGPESFNFYTRRKVVT 495

Query: 513 EMY 515
             +
Sbjct: 496 SRW 498


Lambda     K      H
   0.316    0.134    0.388 

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: 618
Number of extensions: 30
Number of successful extensions: 4
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: 515
Length of database: 513
Length adjustment: 35
Effective length of query: 480
Effective length of database: 478
Effective search space:   229440
Effective search space used:   229440
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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