GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Desulfovibrio vulgaris Miyazaki F

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 8501639 DvMF_2357 AMP-binding domain protein (RefSeq)

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



>FitnessBrowser__Miya:8501639
          Length = 550

 Score =  175 bits (443), Expect = 5e-48
 Identities = 166/565 (29%), Positives = 252/565 (44%), Gaps = 81/565 (14%)

Query: 20  LERAATVYGDCTSVVYDAVSYTWSQTHRRCLC----LASSIASLGIENGHVVSVLAPNVP 75
           L+     Y D  +V+Y  V   + QT+R+       LA  + +LG+ +G  V+V A NVP
Sbjct: 15  LDETVAKYPDNDAVIY--VDRDYRQTYRQFSQVVDDLAKGLMALGVRHGEKVAVWATNVP 72

Query: 76  QMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFV-----DHLSRDLILEAIA 130
               L FA    GAIL  VN       I  LL  SE + +F+     DH   D +     
Sbjct: 73  YWVALQFATAKMGAILLTVNTNYREHEIRYLLTQSECENLFIIDGFRDH---DYVQTIYN 129

Query: 131 LFPKQAPVPR-------------LVFMADESESGNSSE---LGKEFFCSYKDLIDRG--- 171
           + P+    PR             ++F+  E   G  S    +      S ++  +R    
Sbjct: 130 MIPELKTQPRGQLRCSSLPHLKRVMFLGAEKHRGMYSVPEIISMSAMVSDEEYAERQRAL 189

Query: 172 DPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCH-----RGIFIMTVDSLIDWGVPKQP 226
           DP           D + + YTSGTT  PKGV+  H      G +I       +    K  
Sbjct: 190 DPH----------DVVNMQYTSGTTGFPKGVMLTHVNIGNNGYWIGKNQHFTE----KDR 235

Query: 227 VYLWTLPMFHANGWSYPWGMAAV--GGTNICLRKFDSEIIYDMIKRHGVTHMCGAP---- 280
           V L  +P+FH  G      +AA+  G   + L  F    +   + +   T + G P    
Sbjct: 236 VCL-PVPLFHCFGCVLGV-LAAINHGAALVILESFSPMHVMASVDQEKCTALYGVPTMFL 293

Query: 281 -VVLNMLSNAPGSEPLKTTVQIMTAGAPPPSAVLFRTESLGFA--VSHGYGLTETAGLVV 337
            V+ + L        L+T +    AG+  P  ++ R     +   ++  YGLTE + ++ 
Sbjct: 294 AVLEHKLFERFDFSSLRTGIM---AGSVCPEPLMRRVVEKMYMREITICYGLTEGSPVMT 350

Query: 338 SCAWKKEWNHLPATERARLKSRQGVGTVMQT-KIDVVDPVTGAAVKRDGSTLGEVVLRGG 396
                  +           +  Q VG  M   ++ +VDP T   V R   T GEVV RG 
Sbjct: 351 QSLVTDPFE----------RRVQTVGRAMPCIEVRIVDPDTNEEVPR--GTQGEVVCRGY 398

Query: 397 SVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVE 456
           +VM GY   PE T  ++ ADGW ++GD+GVM  +GY+ I  R KD+II GGEN+   E+E
Sbjct: 399 NVMKGYYNMPEATTAAIDADGWLHSGDLGVMDEEGYVVITGRIKDMIIRGGENIYPREIE 458

Query: 457 SILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPK 516
             LY    + +  VV      +GE   AF+  K G+   P  +++ +YCR ++  + VP+
Sbjct: 459 EFLYGMDGVQDVQVVGVNSRKYGEEVGAFIIPKPGVEMAP--EDVRDYCRGRIAWHKVPR 516

Query: 517 TVVFKEELPKTSTGKVQKFILRDMA 541
            + F +  P T++GK+QKF LR+MA
Sbjct: 517 YISFIDAYPMTASGKIQKFKLREMA 541


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: 703
Number of extensions: 36
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: 550
Length adjustment: 36
Effective length of query: 520
Effective length of database: 514
Effective search space:   267280
Effective search space used:   267280
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