GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Bacillus altitudinis 41KF2b

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_019744147.1 BA79_RS03900 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= curated2:Q2SXN9
         (487 letters)



>NCBI__GCF_000691145.1:WP_019744147.1
          Length = 486

 Score =  188 bits (477), Expect = 4e-52
 Identities = 141/447 (31%), Positives = 213/447 (47%), Gaps = 9/447 (2%)

Query: 5   FIDGAWVDG-AGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARC 63
           +I G WVD       A  NP T E + E   ++  DVE AV +A+ AF  WS   +  R 
Sbjct: 12  YIGGQWVDAETNQTEAVYNPATGEVIAEVPLSTKTDVEHAVQAAQEAFTTWSKTAVPRRA 71

Query: 64  TIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAP 123
            I+ ++  LLVE+ + LA ++  E GK + EA+ EV      V+ +  A     G++   
Sbjct: 72  RILFKYQQLLVEKWDELAELVTLENGKSVTEAKGEVQRGIECVEFAAGAPTLMMGKQLPD 131

Query: 124 MADGVAVLRHR-PHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATV 182
           +A G+    +R P GV+    P+NFP  +P      A+  GNT V KPSE  P +A    
Sbjct: 132 IATGLESGMYRYPIGVIGGITPFNFPMMVPCWMFPLAIACGNTFVLKPSERTPILAARLA 191

Query: 183 EIWRDAGLPAGVLNLVQGEKDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242
           E++ +AGLP GVLN+V G  D    L  H ++  + F GS      ++K+     + V A
Sbjct: 192 ELFEEAGLPKGVLNIVNGAHDVVNGLLEHEKVKAISFVGSQPVAEYVYKKGTAHGKRVQA 251

Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302
           L  G  N  +V +  D+++A    I +AF SAG+RC  A  + V      D  + +L D 
Sbjct: 252 L-AGAKNHSIVLKDADLESATKQIIGAAFGSAGERCMAAAVVAVEEDV-ADDLIQQLVDE 309

Query: 303 ASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPALG---FV 359
           ++++       +   F+G VI      R +      +  GAS I + +Q +   G   FV
Sbjct: 310 SNQLVIG-NGINKDVFLGPVIRKEHKERTLQYIQSGIEEGASLIRDGRQDNETNGEGYFV 368

Query: 360 NAAILD-VTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWHT 418
              I D VTN  ++  +E F P+  IVR + L +AI  +N + F   A L  D   +   
Sbjct: 369 GPTIFDHVTNQMKIWQDEIFAPVLSIVRVSSLAEAIDLSNQSKFANGACLYTDSASSIRE 428

Query: 419 FRRAIRAGIVNWNRPTNGASSAAPFGG 445
           FR  I AG++  N       +  PF G
Sbjct: 429 FRENIEAGMLGINIGVPAPMAFFPFSG 455


Lambda     K      H
   0.320    0.134    0.402 

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: 439
Number of extensions: 24
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: 487
Length of database: 486
Length adjustment: 34
Effective length of query: 453
Effective length of database: 452
Effective search space:   204756
Effective search space used:   204756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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