GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Acidithiobacillus ferrooxidans ATCC 23270

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>NCBI__GCF_000021485.1:WP_012607209.1
          Length = 506

 Score =  248 bits (632), Expect = 4e-70
 Identities = 156/478 (32%), Positives = 239/478 (50%), Gaps = 20/478 (4%)

Query: 14  FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           FI G WV    GQ   V  P  G+      +  A +   A++AA      W   +  ERA
Sbjct: 22  FIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIADKWGKTSPAERA 81

Query: 74  TKLRRWYELIIENQDDLARLMTLEQGKPLAEA-KGEIVYAASFIEWFAEEAKRIYGDVIP 132
             L +  + I  N + LA   T++ GKP+ E    +I  A     +FA   +   G +  
Sbjct: 82  NILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEGGI-- 139

Query: 133 GHQPDKRLIV--IKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAF 190
               D+  +     +P+GV   I PWNFP  M + K  PAL AG  +VLKPA  TP S  
Sbjct: 140 -SDIDENTVAYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPISIL 198

Query: 191 ALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIK 250
            LAEL     +P GV ++V+G   + G  L ++  + K++FTGST  GR +    A  + 
Sbjct: 199 ILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAANSLI 257

Query: 251 KVSLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDA 304
             +LELGG +P I F      DD+ LDKA+EG ++  + N G+ C C +R  IQ+ +YD 
Sbjct: 258 PATLELGGKSPNIFFADVMDKDDSFLDKAIEGLVLFAF-NQGEVCTCPSRALIQESIYDK 316

Query: 305 FAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGK----- 359
           F E+    +  +K GN L+  T  G    ++ + K+  ++     +GA VL GG      
Sbjct: 317 FMERCLDRIKAIKQGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEGAQVLIGGSQAIVD 376

Query: 360 -PMEGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYA 418
             ++G ++    L    N   + +EE FGP+  +  FKDEA+ ++++NDT +GL +  ++
Sbjct: 377 GDLDGGYYVQPTLFKGHNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGAGVWS 436

Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476
           R+    +R+  A++ G V +N        A FGG K SG+GRE  K  ++ Y + K L
Sbjct: 437 RNGNVAYRMGRAIKAGRVWINCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQQTKNL 494


Lambda     K      H
   0.317    0.135    0.390 

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: 576
Number of extensions: 28
Number of successful extensions: 7
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: 480
Length of database: 506
Length adjustment: 34
Effective length of query: 446
Effective length of database: 472
Effective search space:   210512
Effective search space used:   210512
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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