GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Desulfacinum infernum DSM 9756

Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_073041560.1 BUB04_RS16575 FAD-dependent oxidoreductase

Query= BRENDA::Q5JFG2
         (385 letters)



>NCBI__GCF_900129305.1:WP_073041560.1
          Length = 405

 Score =  179 bits (454), Expect = 1e-49
 Identities = 124/385 (32%), Positives = 192/385 (49%), Gaps = 11/385 (2%)

Query: 2   KSEAKTVIIGGGIIGLSIAYNLAKL-GESDIVVLEKGYLGNGSTFRCGTGIRQQFGDEAN 60
           +S    VI+GGG+ GL+ AY LAK  G   + VLEK ++G GS  R    +R     + N
Sbjct: 15  RSTYDAVIVGGGLHGLATAYYLAKNHGVRRVAVLEKNHIGYGSAGRNTAIVRANQRTQEN 74

Query: 61  IRMMKRSVELWKGLKEELGYDVEFTQSGYLFLIYSEEELEAFNNNVRLQNRFGVPSRIIT 120
           I +    +++W  L +EL +++ F   G L L +SE  + A    V      GV S ++ 
Sbjct: 75  IPLYDEGLKMWPQLMDELDFNLMFFNCGNLNLAHSEAAMGALRLQVASAQYLGVRSELLD 134

Query: 121 PEEAKEIVPPLN-----TDGVIAAAWNHTDGKANPFKAVFAYANAAKRLGVEIYEYTEAK 175
            ++ KE++P LN     T  V    ++   G       V+A A  A  LGV I++ TE  
Sbjct: 135 RKQCKELIPHLNISEDITYPVFGGMYHPPGGTVRHDALVWALAKGASALGVHIHQQTEVT 194

Query: 176 DIKVEDGKIKAVVTNRGEIRTGRVINAANAWAPLINKMAGVPIKIPIEPYKHQSVKTEPI 235
            I V  G++ AV T+RG I T RV+NAA  W+ L++ M  V I++PI     Q++ TEP+
Sbjct: 195 GIAVHRGRVTAVETSRGTIHTLRVLNAAGPWSVLVSAM--VDIRLPIHVLPIQAMVTEPL 252

Query: 236 KPGQIEPMVISFKHGGVYMTQEANQGGVIGGYGLKYGPTYDITPTYDFLRGVSYRFAQII 295
           KP      VIS      Y  Q   +G V+ G  +    +Y    T  +++  +    +++
Sbjct: 253 KP--FLHHVISSGAYHCYANQSL-KGEVVTGAHMDPWISYGTHVTAHYIKHQAEALTELL 309

Query: 296 PALKYVNIIRVWGGFYAETPDHNAAIGRINEIDEFYIAAGFSGHGFMLAPVVGEALAELI 355
           P L+ V  +R+WGG    TPD    I   + I+ +Y+  G+   GF  A V G+ +AE +
Sbjct: 310 PCLRGVKFMRIWGGLADMTPDMAPIIDGNDPIEGYYMDCGWGYFGFKSAAVTGKYVAEYM 369

Query: 356 VDGKTDKPLDFYDPYRFERGELRGQ 380
             G+  K L  +   R+E   L G+
Sbjct: 370 ATGRCPKILQPFRLKRYEENRLLGE 394


Lambda     K      H
   0.318    0.139    0.412 

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: 371
Number of extensions: 13
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: 385
Length of database: 405
Length adjustment: 31
Effective length of query: 354
Effective length of database: 374
Effective search space:   132396
Effective search space used:   132396
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 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