GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Paraburkholderia bryophila 376MFSha3.1

Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate H281DRAFT_06542 H281DRAFT_06542 4-methylaminobutanoate oxidase (formaldehyde-forming)

Query= BRENDA::Q76M73
         (385 letters)



>FitnessBrowser__Burk376:H281DRAFT_06542
          Length = 826

 Score =  153 bits (386), Expect = 2e-41
 Identities = 113/390 (28%), Positives = 178/390 (45%), Gaps = 23/390 (5%)

Query: 5   AKTVIIGGGIIGLSIAYNLAKLGESDVVVLEKGYLGNGSTFRCGTGIRQQFNDEANIRMM 64
           A+ VIIGGGIIG S+AY+L KLG +DVV+LE+G L  G+T+     + Q    E+  +++
Sbjct: 9   ARVVIIGGGIIGCSVAYHLTKLGWTDVVLLEQGQLSCGTTWHAAGLVGQLRAQESMTKLI 68

Query: 65  KRSVELWKGLSEELGMDVEFTQSGYLFLIYEKDELEAFKNNVRLQNRFGVPSRIITPEEA 124
           + S  L+  L  E G+   + Q G L +    + +   K    +   +GV   +I   EA
Sbjct: 69  RYSTALYAELEAETGLATGWKQCGSLSVARTAERMTQLKRTAAVARAYGVACDVIGAREA 128

Query: 125 KEIVPPLNTNGVIAAAWNHTDGKANPFKAVFAYAEAAKRLGVEIYEYTEAKDIRVEEGKI 184
            ++ P + T+ ++ A W   DGKANP     A A  A+  G  I E T        +   
Sbjct: 129 GDLWPVMRTDDLLGAVWLPGDGKANPTDLTQALARGARMRGARIVENTRVTATHTRDAHG 188

Query: 185 KTVVT---------NRGEIKTGRVINAANAWAPLINKMAGVPIKIPIEPYKHQGVKTEPI 235
               T         + G I    V+N A  WA  + ++  V   +P+   +H  + TE I
Sbjct: 189 AREATGVAWRNKDGDEGTIGAEIVVNCAGQWAKAVGRLCDV--TVPLHSAEHYYIVTERI 246

Query: 236 KPGQIEPMVISFKHGGVYLTQEAYQGGVIGGY----------GLKYGPTYDITP-TYEFL 284
                +  V+    G +Y  +E   G V+GG+          G+     + + P  ++  
Sbjct: 247 AGVHPDLPVMRDPDGFIYFKEEV-GGLVMGGFEPNAKPWGMQGIPEHFEFQLLPDDWDQF 305

Query: 285 RGVSYRFSQIIPALKYVNVIRIWGGFYAETPDHNAAIGRINEIDEFYIAAGFSGHGFMLA 344
             +     Q +PAL+   V + + G  + TPD+N  +G   E+  F++ AGF+  G   A
Sbjct: 306 EILMTNALQRVPALETAQVRQFYNGPESFTPDNNFMLGEAPELRRFFVGAGFNSMGIASA 365

Query: 345 PAVAEALAEFIVDGKTDKPLDFYDPYRFER 374
                ALAE+IV G+    L   D  RF R
Sbjct: 366 GGAGMALAEWIVAGEPTMDLWPVDIRRFAR 395


Lambda     K      H
   0.319    0.139    0.411 

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: 634
Number of extensions: 36
Number of successful extensions: 3
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: 385
Length of database: 826
Length adjustment: 36
Effective length of query: 349
Effective length of database: 790
Effective search space:   275710
Effective search space used:   275710
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: 53 (25.0 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