GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Limnohabitans curvus MWH-C5

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_108401501.1 B9Z44_RS01335 cyclohexanecarboxylate-CoA ligase

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>NCBI__GCF_003063475.1:WP_108401501.1
          Length = 547

 Score =  215 bits (547), Expect = 4e-60
 Identities = 168/548 (30%), Positives = 264/548 (48%), Gaps = 31/548 (5%)

Query: 28  EQTIGAFFADMVARQPEREALVSVH----QGRRYTYAQLQTEAHRLASALLGMGLTPGDR 83
           ++TI       VA  P++ AL +V     +  R+TY +L   A R+A  L  +G+   D 
Sbjct: 23  DRTINDDLDACVATCPDKLALTAVQAESGKVTRFTYRELSNMADRVALGLTKLGVGQNDI 82

Query: 84  VGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDY 143
           V     N  ++ +  LA +++G V+  +   +R  E+ + L     K+L+    F+  DY
Sbjct: 83  VACQLPNWWQFTITYLACSRIGAVMNPLMHIFRERELSFMLKHGEAKVLIIPQTFRGFDY 142

Query: 144 LGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAAD 203
             M+ E+ P              LP LK VV ++   G GA+    L       + + A 
Sbjct: 143 EKMVNEIKPS-------------LPDLKHVVVVN---GAGANSFEALLSGPAWEKESNAT 186

Query: 204 PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIP 263
             L Q   G    D   + +TSGTTG PKG   T   ++ N       + L   D + + 
Sbjct: 187 AVLTQHRPG--PDDVTQLIYTSGTTGEPKGVMHTANTVMANIIPYAARLHLDANDVVLMA 244

Query: 264 VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAEL-D 322
            P+ H  G + G +      ++ V   D ++PL  +  ++ E  T      T F+ +L  
Sbjct: 245 SPMAHQTGFMYGLMMPIMLKSSAVLL-DVWEPLRAIDLIRHEGAT-FTMASTPFLTDLAK 302

Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382
           +   +   + TLRT + AG+P P  ++++    +  + I  A+GMTE   V+     D P
Sbjct: 303 NVEESGKKVPTLRTFLCAGAPIPGPLVEQARSVLGTK-IVSAWGMTENGAVTLIELND-P 360

Query: 383 LSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDE 442
             +  +T G   P +E+K+V+ D GAV+P G+ G+   +  S   GY   +       D 
Sbjct: 361 DERAFTTDGLPLPGVELKVVNDD-GAVLPAGEAGKLYVRSCSNFGGYL--KRAHLNGTDA 417

Query: 443 GGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPD 502
            GW  TGDLA +DA+GYV I GR KD++IRGGENI   EIE  LYRHP +    +V  PD
Sbjct: 418 EGWFDTGDLARLDAQGYVRITGRSKDVIIRGGENIPVVEIESLLYRHPAIAMAAIVAYPD 477

Query: 503 QKYGEELCAWIIAKPGTQPTEDDIRAFCKGQ-IAHYKVPRYIRFVTSFPMTVTGKIQKFK 561
           ++ GE  CA ++ KPG       +  + K Q IA   +P  +    + P T +GKIQKFK
Sbjct: 478 ERLGERACAVVVLKPGQSLDLPALVDYLKAQKIALQYIPEKLEIRDAMPATPSGKIQKFK 537

Query: 562 IRDEMKDQ 569
           +R+ ++D+
Sbjct: 538 LREILRDE 545


Lambda     K      H
   0.320    0.136    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: 673
Number of extensions: 40
Number of successful extensions: 5
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: 578
Length of database: 547
Length adjustment: 36
Effective length of query: 542
Effective length of database: 511
Effective search space:   276962
Effective search space used:   276962
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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