GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Pseudomonas stutzeri RCH2

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate GFF3731 Psest_3800 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_091789
         (282 letters)



>FitnessBrowser__psRCH2:GFF3731
          Length = 508

 Score =  207 bits (526), Expect = 5e-58
 Identities = 115/280 (41%), Positives = 164/280 (58%), Gaps = 1/280 (0%)

Query: 2   KKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEAT 61
           +++ V+GAG MG GIAQ FA  G +V L D + E +   L F  + L + V KG++  A 
Sbjct: 3   ERIGVVGAGAMGRGIAQLFAGAGKQVWLHDSRSESISDALRFNRELLERGVAKGRLSVAE 62

Query: 62  KVEILTRISGTVDLNMAADCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLSI 121
               L R+     L   + CDLVIEA VE ++IK+ +F +L+ +   + +LA+NTSSLS+
Sbjct: 63  LDATLARMQAAPALADLSGCDLVIEAIVENLEIKQALFVELEALLAEDAVLATNTSSLSV 122

Query: 122 TEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEVAE 181
           T +A+A + P +V G HFFNP P+MKLVEV+RG  +  +    + + +   G  P    +
Sbjct: 123 TRIAAACRLPGRVAGFHFFNPVPLMKLVEVVRGERSDPQVIQRLVKLAEDAGHFPAITPD 182

Query: 182 APGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICLAI 241
            PGF+VN        EA  ILAEGIA  E ID+ ++ G    MGP EL D  GLDI  A+
Sbjct: 183 TPGFLVNHAGRAYSTEAQRILAEGIADAEQIDRILRDGPGFRMGPFELFDLTGLDISHAV 242

Query: 242 MDVLYSE-TGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDY 280
           M+ +Y +   D +Y P     + V AG LGRK+G+G+Y Y
Sbjct: 243 MESVYQQFYQDPRYTPSYQAAQRVAAGLLGRKTGQGYYRY 282



 Score = 57.8 bits (138), Expect = 5e-13
 Identities = 34/99 (34%), Positives = 56/99 (56%), Gaps = 4/99 (4%)

Query: 171 AIGKD--PVEVA-EAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPL 227
           A+G D  PVEV  ++PGFV  R++  ++N    I  +GIA  + +D+A+ L   +P GPL
Sbjct: 395 ALGSDGVPVEVINDSPGFVSQRVVASIVNLGCEIAQKGIADPQTLDRAVTLALGYPKGPL 454

Query: 228 ELGDFIGLDICLAIMDVLYS-ETGDSKYRPHTLLKKYVR 265
              +  G    LAI+  +     G+++YRP   L++ V+
Sbjct: 455 GFAEHYGAARILAILQAMQGCYGGEARYRPSPWLRRRVQ 493


Lambda     K      H
   0.319    0.137    0.386 

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: 348
Number of extensions: 13
Number of successful extensions: 3
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: 282
Length of database: 508
Length adjustment: 30
Effective length of query: 252
Effective length of database: 478
Effective search space:   120456
Effective search space used:   120456
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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