GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Granulicella mallensis MP5ACTX8

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_150110902.1 ACIX8_RS16850 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-15203
         (503 letters)



>NCBI__GCF_000178955.2:WP_150110902.1
          Length = 789

 Score =  239 bits (609), Expect = 3e-67
 Identities = 156/476 (32%), Positives = 251/476 (52%), Gaps = 34/476 (7%)

Query: 8   HYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRR 67
           HYI+G  T  V+ S  E  NPATG+V  ++A A  +DVD AV AA+AA PAW      +R
Sbjct: 26  HYIDGAWTQ-VSGSSFETRNPATGEVLAKIATADASDVDRAVKAARAALPAWQALTGHQR 84

Query: 68  ARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFA------CGIPQLL 121
           AR ++ F   +  H   LA   T ++GK   ++     R IDI   A       G  QLL
Sbjct: 85  ARYLYAFARQVQKHARRLAVLETLDNGKSIRES-----RDIDIPLVARHFYHHAGWAQLL 139

Query: 122 KGDYTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDP 181
             ++    S           +GVV  I P+NFP+++  W    A+AAGN+ V+KP+   P
Sbjct: 140 DEEFPGYTS-----------VGVVGQIIPWNFPLLMFAWKVAPALAAGNTVVIKPAEFTP 188

Query: 182 SASLMMADLLKQAGLPDGVFNVVQGDKDSVEALIDHPDVKALSFVGSTPIANLIYERGAR 241
            ++L +A++ ++ GLP GV NV+ GD  +  A+++H D+  ++F GST +  +I +  A+
Sbjct: 189 LSALALAEIAQEIGLPKGVLNVINGDGKTGAAIVEHTDIDKIAFTGSTEVGRIIRKATAK 248

Query: 242 SGKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVP 301
           + K++    G K+  +V  DA+LD  V+ L+   + + G+ C A S  ++   VA+K+  
Sbjct: 249 TSKKLSLELGGKSPFIVFDDADLDSTVEGLVDGIWFNQGQVCCAGSRLLVQERVAEKLYD 308

Query: 302 RLAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTG 361
           ++  R   L++ + L+   ++G IV    + RI G +E GV EGA        +   VT 
Sbjct: 309 KIRSRMETLRVGSPLDKAIDIGAIVDQIQYDRIKGLVETGVKEGATC------WQPEVTM 362

Query: 362 EGCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCF 421
                G +   TL  +V P  T+ +EEIFGPVL  +     A A++L N+  +G     +
Sbjct: 363 P--EKGLFFKPTLLTNVHPASTVAQEEIFGPVLVSMTFRTPAEAVELANNTTYGLAACVW 420

Query: 422 TESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFY 477
           +E+ +VA +   +++ G+V +N       A  GFGG++ S +G     G+EG+  Y
Sbjct: 421 SENINVALDVAAQVKAGVVWVNATNLFDAAC-GFGGYRESGYG--REGGKEGMYEY 473



 Score = 51.2 bits (121), Expect = 1e-10
 Identities = 46/197 (23%), Positives = 88/197 (44%), Gaps = 10/197 (5%)

Query: 31  GQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRRARVMFKFLELLNAHKDELAEAIT 90
           GQ+ G+  L ++ D+ +AV AA+     W+ T    RA++++   E +   + E+   + 
Sbjct: 539 GQLVGEAPLGNRKDIRNAVEAARNISAKWAKTTAHGRAQILYYIAENMVQRRAEIVAKLA 598

Query: 91  REHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPLGVVAGITP 150
              G     A  E+  G++            +G         +     ++ +G V  + P
Sbjct: 599 AFVGP--EQAAIELDYGVERTFAYAAWADKFEGS-VHNPPMRMVTLAMKEAIGTVGILCP 655

Query: 151 FNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMMADLLK---QAGLPDGVFNVVQGD 207
            + P++  + +   AIA GN+ V  PS      + +M+DL +    + LP GV N+V G 
Sbjct: 656 DDAPLLGFLSLVLPAIAMGNAVVAVPS---ERCATLMSDLYQVFDTSDLPGGVVNIVAGK 712

Query: 208 KDSV-EALIDHPDVKAL 223
              + + L +H D+ A+
Sbjct: 713 ASELGKTLAEHDDIDAI 729


Lambda     K      H
   0.319    0.136    0.406 

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: 919
Number of extensions: 48
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 503
Length of database: 789
Length adjustment: 38
Effective length of query: 465
Effective length of database: 751
Effective search space:   349215
Effective search space used:   349215
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: 54 (25.4 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