GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Bacillus altitudinis 41KF2b

Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate WP_035391821.1 BA79_RS18270 glycolate oxidase subunit GlcD

Query= reanno::Smeli:SMc00832
         (479 letters)



>NCBI__GCF_000691145.1:WP_035391821.1
          Length = 469

 Score =  325 bits (832), Expect = 3e-93
 Identities = 173/430 (40%), Positives = 256/430 (59%), Gaps = 2/430 (0%)

Query: 44  FETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIV 103
           +  DA   +++MP A+V P T E V  ++K C+ Y +PIVPRG+GT+L  G  P +  +V
Sbjct: 29  YSYDATPNFQQMPDAIVRPHTAEEVQQIVKLCASYKVPIVPRGSGTNLCAGTCPTQGGLV 88

Query: 104 VGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMN 163
           +  ++M++ L+ID  N TATVQ G+    +   V   G FY PDPSS    T+GGNI  N
Sbjct: 89  ILFTRMNQLLEIDEENLTATVQPGLITQELIHQVEEKGLFYPPDPSSMKISTLGGNINEN 148

Query: 164 SGGAHCLKYGVTTNNLLGVKMVLFDGTVIELGGK-ALDAPGYDLLGLVCGSEGQLGIVTE 222
           SGG   LKYGVT + +LG+++VL +G +I+ GGK A D  GYD+  L  GSEG LGIVTE
Sbjct: 149 SGGLRGLKYGVTRDYVLGLEVVLPNGDIIKTGGKLAKDVAGYDMTRLFVGSEGTLGIVTE 208

Query: 223 ATVRLIAKPEGARPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQAG 282
           A ++L+  PE  + +L  + S E A + V+ II   IIP  +EFMD+P +E+ E FA  G
Sbjct: 209 AVLKLLPLPETKQTMLCLYESLEEAATSVSAIIAERIIPATLEFMDQPTLEVVEDFANIG 268

Query: 283 YPLDVEALLIVEVEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAFG 342
            P DV+A+L++E +G+   +   +  I E+  +HG  +++ + S  EA+ +   R+SA  
Sbjct: 269 LPTDVQAVLLIEQDGNPEAVSRDIQKIAEVCEQHGATSVKIAHSEEEASALLTARRSALS 328

Query: 343 ATGRIA-DYICMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILYNIND 401
           A  R++   I  D TVP S++++++R   +I   Y + +    HAGDGN+HP    +  +
Sbjct: 329 ALARLSPTTILEDATVPRSEIANMVRAIEDIARKYEVNICTFGHAGDGNLHPTCATDARN 388

Query: 402 PEEAARAEAAGNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDP 461
            EE  R EAA   I +  V  GG +TGEHGVG+ K   +  +  +  +    A + A DP
Sbjct: 389 EEEMKRVEAAFQAIFEKAVALGGTITGEHGVGLMKAPYLELKVKKEGIAAMKAIKQALDP 448

Query: 462 QWLMNPSKVF 471
             +MNP KVF
Sbjct: 449 AHIMNPDKVF 458


Lambda     K      H
   0.320    0.138    0.404 

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: 525
Number of extensions: 19
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: 479
Length of database: 469
Length adjustment: 33
Effective length of query: 446
Effective length of database: 436
Effective search space:   194456
Effective search space used:   194456
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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