GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Acidithiobacillus ferrooxidans ATCC 23270

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase

Query= BRENDA::B6ECN9
         (505 letters)



>NCBI__GCF_000021485.1:WP_012607209.1
          Length = 506

 Score =  326 bits (836), Expect = 1e-93
 Identities = 195/482 (40%), Positives = 276/482 (57%), Gaps = 18/482 (3%)

Query: 14  FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73
           FI G+W  P+K     +I P N +       +T ED+++A+ AA +    D WG T+ A+
Sbjct: 22  FIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIA--DKWGKTSPAE 79

Query: 74  RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEAAS-DIDDVVACFEYYADLAEALDSKK 132
           RA  L  +A ++      LA  ET+DNGKP  E  + DI   V  F Y+A    A +   
Sbjct: 80  RANILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEGGI 139

Query: 133 QTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSELASI 192
            +++  +  ++  H   EPLGVVG I PWN+P+LM +WK+APAL AG   +LKP+E   I
Sbjct: 140 -SDIDENTVAYHFH---EPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPI 195

Query: 193 TSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMTAAAQ 252
           + L L E+  ++ LPPG L+I+ G G EAG PL +   + KIAFTGS  TG  I  AAA 
Sbjct: 196 SILILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAAN 254

Query: 253 LVKPVTLELGGKSPIVVFDDIHN-----LDTAVEWTLFGCFWTNGQICSATSRLIIQETI 307
            + P TLELGGKSP + F D+ +     LD A+E  +   F   G++C+  SR +IQE+I
Sbjct: 255 SLIPATLELGGKSPNIFFADVMDKDDSFLDKAIEGLVLFAF-NQGEVCTCPSRALIQESI 313

Query: 308 APQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYGGDRP 367
             +F+ R L+  K IK  +PL+ +  +G   S+ Q  KIL ++   K EGA +L GG + 
Sbjct: 314 YDKFMERCLDRIKAIKQGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEGAQVLIGGSQA 373

Query: 368 ---EHLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKFGLGA 424
                L  GYY+QPT+       M I++EE+FGPVL V TFK E EA+ +ANDT +GLGA
Sbjct: 374 IVDGDLDGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGA 432

Query: 425 AILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENYLNIK 484
            + S++     R  +A ++G VWINC         +GG K SG GRE  +  L++Y   K
Sbjct: 433 GVWSRNGNVAYRMGRAIKAGRVWINCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQQTK 492

Query: 485 QV 486
            +
Sbjct: 493 NL 494


Lambda     K      H
   0.318    0.136    0.421 

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: 609
Number of extensions: 29
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: 505
Length of database: 506
Length adjustment: 34
Effective length of query: 471
Effective length of database: 472
Effective search space:   222312
Effective search space used:   222312
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.

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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