GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudarthrobacter sulfonivorans Ar51

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058929219.1 AU252_RS01520 AMP-binding protein

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



>NCBI__GCF_001484605.1:WP_058929219.1
          Length = 537

 Score =  618 bits (1593), Expect = 0.0
 Identities = 310/559 (55%), Positives = 389/559 (69%), Gaps = 26/559 (4%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75
           S+ +GA   PL+ +TIG  F   VA+    EALV V  GRR+T+A+L  + + LA  L+ 
Sbjct: 3   SYEKGAVVPPLLSETIGQSFERTVAQYSGNEALVEVASGRRWTWAELDRDVNDLAKGLVA 62

Query: 76  MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135
            GL  GDR+GIW+ N AEW L+Q ATA++G++LVN+NPAYRT E  YA+N  G ++L++ 
Sbjct: 63  AGLEKGDRLGIWAPNCAEWTLVQYATAKIGVILVNVNPAYRTHEFSYAVNHSGLRMLITA 122

Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
           + FK+SDY  M+ + A E              P L+ V +ID +            +  L
Sbjct: 123 SSFKSSDYRAMIEQAADE-------------TPSLERVAYIDTDD-----------WAHL 158

Query: 196 IARGNAADPRL-AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254
           I  G   +  + AQ  A     DPINIQ+TSGTTG+PKGATL+HRNILNNG+F  E ++L
Sbjct: 159 IDSGRTVENHVVAQRLADTMPDDPINIQYTSGTTGYPKGATLSHRNILNNGYFTTELIRL 218

Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314
            P DRLCIPVP YHCFGMV+G+L C +HG TIV P+ GFD    L+ + DE+CT ++GVP
Sbjct: 219 GPDDRLCIPVPFYHCFGMVMGSLGCVSHGTTIVIPSPGFDAEATLRAITDEKCTAVYGVP 278

Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374
           TMFIA  +HP F   +L++LRTGIMAGS CP +VM+R +E MNL EI+IAYGMTETSPVS
Sbjct: 279 TMFIAMQNHPTFGSHDLTSLRTGIMAGSVCPVDVMQRCIEDMNLTEISIAYGMTETSPVS 338

Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434
           CQ+  +  + +R +T+G+V PHLEVKIVDP TG  V   Q GEFCT+GYSVM GYW DE 
Sbjct: 339 CQTRANDDVERRTATIGRVHPHLEVKIVDPSTGDTVERDQTGEFCTRGYSVMLGYWNDEE 398

Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494
           KTREAID  GWMHTGDL  M  +GY  IVGRIKDMVIRGGENIYPREIEE+LY HP ++D
Sbjct: 399 KTREAIDADGWMHTGDLGVMREDGYCTIVGRIKDMVIRGGENIYPREIEEYLYSHPDIED 458

Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTE-DDIRAFCKGQIAHYKVPRYIRFVTSFPMTV 553
           VQV+GVPD KYGEELCA I  K GT+P +   IRAF  G+IA YK+P Y+  V  FP TV
Sbjct: 459 VQVIGVPDAKYGEELCACIKMKAGTKPLDAPAIRAFINGKIARYKIPVYVIVVDEFPTTV 518

Query: 554 TGKIQKFKIRDEMKDQLGL 572
           TGKI+K ++R+E    LGL
Sbjct: 519 TGKIRKNQLREEASTVLGL 537


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: 843
Number of extensions: 36
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: 537
Length adjustment: 36
Effective length of query: 542
Effective length of database: 501
Effective search space:   271542
Effective search space used:   271542
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 Apr 09 2024. 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