GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Duganella sacchari Sac-22

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_072791060.1 BUA36_RS29590 long-chain-fatty-acid--CoA ligase

Query= metacyc::MONOMER-20125
         (556 letters)



>NCBI__GCF_900143065.1:WP_072791060.1
          Length = 563

 Score =  163 bits (413), Expect = 1e-44
 Identities = 160/562 (28%), Positives = 240/562 (42%), Gaps = 71/562 (12%)

Query: 20  LERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYE 79
           LE +   Y +  + V      T+++       L + + S G++ G  V+++ PNV Q   
Sbjct: 29  LEESFHKYANRNAYVCMDKFLTYAEVDAYSKRLGAWLQSRGLKPGARVAIMMPNVLQYPI 88

Query: 80  LHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQA--- 136
              A+  AG  +  VN     R +   L+ S S+ I        +ILE  A   +Q    
Sbjct: 89  AIAAILRAGYTVVNVNPLYTPRELEHQLNDSGSEAI--------IILENFATTLEQVLGR 140

Query: 137 -PVPRLVFMADESESGNSSELGKEFFCS----------------YKDLIDRGDPDFKWVM 179
             V  +V  +     G    +   F                   +KD + +G       +
Sbjct: 141 TQVKHIVVASMGEMLGGLKGMLVNFVVRSVKKMVPAFSLPNAVRFKDALSQGGGMKLTPV 200

Query: 180 PKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVP------KQPVYLWTLP 233
            +   DP  L YT GTT   KG    H+ I    + S   W  P      +Q   +  LP
Sbjct: 201 ERQYNDPAFLQYTGGTTGVSKGATLTHQNIVANLLQSEA-WSQPALGGSDEQVTIVCALP 259

Query: 234 MFHANGWSY--PWGMAAVGGTNICL-RKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP 290
           ++H    +    WG   VG  NI +    D       + ++    +     + N L N P
Sbjct: 260 LYHIFALTACAMWG-TRVGALNILIPNPRDIGGFIKELAKYKFNMLPAVNTLYNALLNHP 318

Query: 291 GSEPLK-TTVQIMTAGAPP-PSAVLFR-TESLGFAVSHGYGLTETAGLVVSCAWKKEWNH 347
               L  + ++I   G      AV  R  ++ G ++  GYGL+ET+              
Sbjct: 319 DFVHLDFSALKICNGGGMAVQQAVNDRWLKATGVSIIEGYGLSETS-------------- 364

Query: 348 LPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGS------TLGEVVLRGGSVMLG 401
            P     R  S    GT     I +  P T  A+  D        T GE+ +RG  VM G
Sbjct: 365 -PVATCNRADSTAFTGT-----IGLPVPSTDIAILDDDGNEVALGTAGEIAIRGPQVMAG 418

Query: 402 YLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYS 461
           Y   P+ TAK MT DG+F +GDVGVM   GY++I DR KD+I+  G N+   E+E ++ +
Sbjct: 419 YWNRPDETAKVMTPDGFFKSGDVGVMDASGYVKIVDRKKDMILVSGFNVYPNELEGVIAA 478

Query: 462 HPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFK 521
           HP +LE A +  PD++ GE    FV  K       TE E++ YC+ +L  Y  PK + F+
Sbjct: 479 HPGVLECAAIGVPDDYSGEAVKVFVVRK---DPNLTEAELMAYCKEQLTGYKKPKYIEFR 535

Query: 522 EELPKTSTGKVQKFILRDMARG 543
           EELPKT+ GK+ + +LRD A G
Sbjct: 536 EELPKTNVGKILRRMLRDEAPG 557


Lambda     K      H
   0.319    0.135    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: 717
Number of extensions: 31
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: 556
Length of database: 563
Length adjustment: 36
Effective length of query: 520
Effective length of database: 527
Effective search space:   274040
Effective search space used:   274040
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 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