GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Marinobacter algicola DG893

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_007154501.1 MDG893_RS14200 AMP-binding protein

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



>NCBI__GCF_000170835.1:WP_007154501.1
          Length = 562

 Score =  658 bits (1697), Expect = 0.0
 Identities = 323/561 (57%), Positives = 407/561 (72%), Gaps = 7/561 (1%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75
           S+  G ++VPL+  TIGA       + P+ EALV++HQ  R+TY +   + +  A A + 
Sbjct: 7   SYTSGTSEVPLLGMTIGAMLDRTAEKYPDTEALVALHQDIRWTYKEFVEKVNEAARAFIA 66

Query: 76  MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135
           +G+  GDRVGIWS N  EW + Q ATA+VG +LVNINPAY   E++YA+N  G  +LV+ 
Sbjct: 67  IGVKRGDRVGIWSPNRYEWTVTQFATAKVGAILVNINPAYGVHELDYAMNLSGISVLVTA 126

Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
             FK SDY  M+ +LAPE +   PG L+A K+P+L+ VV +D +        G+  + E 
Sbjct: 127 DSFKASDYRKMVYDLAPELKAATPGKLKAQKVPELRAVVNLDKDK-----HDGMWTWAEF 181

Query: 196 IA-RGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254
           I   G+ +   L +V   LQ  DPINIQFTSGTTG PKGATLTH NILNNG+F+ E   L
Sbjct: 182 IGFAGDVSQEELDKVQDQLQFDDPINIQFTSGTTGNPKGATLTHHNILNNGYFVAESQLL 241

Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314
           T  DRL IPVPLYHCFGMV+GNL C THG+T++YP +GF+P +VLQ V  E+ T L+GVP
Sbjct: 242 TEKDRLVIPVPLYHCFGMVMGNLGCITHGSTMIYPGEGFEPKSVLQAVHQEKATALYGVP 301

Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374
           TMFIAEL  P F  ++LSTLRTGIMAGS CP EVMK+V  +MN++E+ IAYGMTETSPVS
Sbjct: 302 TMFIAELAEPEFETYDLSTLRTGIMAGSICPAEVMKKVNGKMNMKEVQIAYGMTETSPVS 361

Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434
            Q+S+  P  K+V+TVG+ QPHLE KIVDP  G VVP G+ GE CT+GYSVM  YW +E 
Sbjct: 362 TQTSSLDPFEKQVTTVGRTQPHLETKIVDPGNGNVVPRGEIGELCTRGYSVMLKYWNNEE 421

Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494
           KT EAID  GWMHTGDLATMD +GY+ IVGRIKDMVIRGGENIYP+EIEEFLY HP +++
Sbjct: 422 KTSEAIDGAGWMHTGDLATMDEDGYIQIVGRIKDMVIRGGENIYPKEIEEFLYTHPAIEE 481

Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQP-TEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTV 553
           VQV G+PD KYGEEL AW+   P   P T D++R FCKG+IAH+K+PR  +FV  FPMTV
Sbjct: 482 VQVTGIPDDKYGEELIAWVKLNPDADPVTGDELREFCKGKIAHFKIPRNYKFVDEFPMTV 541

Query: 554 TGKIQKFKIRDEMKDQLGLEE 574
           TGKIQKFK+R+   +++GL++
Sbjct: 542 TGKIQKFKMREISIEEMGLKK 562


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: 895
Number of extensions: 32
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: 578
Length of database: 562
Length adjustment: 36
Effective length of query: 542
Effective length of database: 526
Effective search space:   285092
Effective search space used:   285092
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.

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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