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::P77674
         (474 letters)



>NCBI__GCF_000021485.1:WP_012607209.1
          Length = 506

 Score =  303 bits (777), Expect = 7e-87
 Identities = 173/471 (36%), Positives = 264/471 (56%), Gaps = 15/471 (3%)

Query: 15  EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVI 74
           +G+   V  P  G    + A ++AE ++ A+ AA A   +WG+T+P  RA  LLK+AD I
Sbjct: 32  KGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIADKWGKTSPAERANILLKVADRI 91

Query: 75  EENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI 134
           E N ++ A  E+ + GKP+    N +IP  VD FR+FAG  R   G    +  E   +  
Sbjct: 92  EANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEG-GISDIDENTVAYH 150

Query: 135 RRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPA 194
             +PLGVV  I PWN+P++MA+WKLAPAL AGN VVLKP+E TP++ L LAEL  D+ P 
Sbjct: 151 FHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPISILILAELIADLLPP 210

Query: 195 GVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVI 254
           GV+NI+ G G+  G PL    ++  ++ TGS  TG  I    A+S+    +ELGGK+P I
Sbjct: 211 GVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAANSLIPATLELGGKSPNI 270

Query: 255 VF------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLK 308
            F      DD+ ++  +EG+  F  +N G+ CT   R   Q+ IYD  +E+    +  +K
Sbjct: 271 FFADVMDKDDSFLDKAIEGLVLFA-FNQGEVCTCPSRALIQESIYDKFMERCLDRIKAIK 329

Query: 309 SGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKR-----KGNGYYYAPT 363
            G P D +T +G  +S   L ++   ++  K  G  +V+ GG +         GYY  PT
Sbjct: 330 QGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEG-AQVLIGGSQAIVDGDLDGGYYVQPT 388

Query: 364 LLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSA 423
           L  G      I Q+E+FGPV++VT F +E + ++ AND+ YGL + VW+++   A+R+  
Sbjct: 389 LFKGH-NKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGAGVWSRNGNVAYRMGR 447

Query: 424 RLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
            ++ G  W+N +    +    GG K SG G++     L+ Y   ++++V +
Sbjct: 448 AIKAGRVWINCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQQTKNLLVSY 498


Lambda     K      H
   0.317    0.134    0.397 

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: 558
Number of extensions: 21
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: 474
Length of database: 506
Length adjustment: 34
Effective length of query: 440
Effective length of database: 472
Effective search space:   207680
Effective search space used:   207680
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