GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Sphingomonas koreensis DSMZ 15582

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Ga0059261_0771 Ga0059261_0771 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II

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



>FitnessBrowser__Korea:Ga0059261_0771
          Length = 554

 Score =  633 bits (1633), Expect = 0.0
 Identities = 313/556 (56%), Positives = 391/556 (70%), Gaps = 24/556 (4%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75
           SH RG    PLIE TIG        +  ER+ALVSV QG R+++A+L     RLAS LL 
Sbjct: 9   SHVRGTDTPPLIEHTIGEALVRAAEQWGERDALVSVAQGIRWSFAELLARTDRLASGLLA 68

Query: 76  MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135
           +GL PG+R+GIWS N AEW L Q A A+ GL+LV INPAYR +EVEY +NKVG   LV+ 
Sbjct: 69  LGLKPGERIGIWSPNCAEWTLTQFAAARAGLILVTINPAYRLSEVEYTINKVGLAALVAA 128

Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
             FKTS Y  M+  L PE            +LP L+  + I +      + PG L F ++
Sbjct: 129 ESFKTSAYAEMVETLGPE------------RLPTLRARILIGEN-----ERPGWLSFADV 171

Query: 196 IARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLT 255
            A    A P        L  +DPINIQFTSGTTG PKGATL+HRNILNNG+F+G  M L+
Sbjct: 172 AAHLAGALPE------DLHPSDPINIQFTSGTTGLPKGATLSHRNILNNGYFVGRGMGLS 225

Query: 256 PADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPT 315
             DR+CIPVPLYHCFGMV+GNLA  THGA +VYP  GFDP   L+ V  ERCT L+GVPT
Sbjct: 226 AQDRICIPVPLYHCFGMVMGNLASLTHGAAMVYPAPGFDPEAALRAVAAERCTALYGVPT 285

Query: 316 MFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSC 375
           MFIA L HP     ++++LRTG MAG+ CP  +M+ V++++++R++TI YGMTETSPVS 
Sbjct: 286 MFIAMLAHPVLDSLDVTSLRTGCMAGAICPEPLMREVIDRLHMRDVTIGYGMTETSPVSF 345

Query: 376 QSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAK 435
           Q++ D P+ +R  ++G+VQPHLE K++D D G +VP+GQ GE CT+GYSVMHGYW ++ +
Sbjct: 346 QTALDDPIHRRTGSIGRVQPHLESKLIDLD-GNIVPVGQPGELCTRGYSVMHGYWDEQER 404

Query: 436 TREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDV 495
           T E+ID  GWMH+GDLA +D EGY NIVGR+KDMVIRGGENIYPREIE FLY HP ++DV
Sbjct: 405 TAESIDAEGWMHSGDLAVIDDEGYANIVGRLKDMVIRGGENIYPREIEGFLYSHPAIEDV 464

Query: 496 QVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTG 555
            VVGVPD + GEELCAW+  + G Q   + IR FC+GQIAH+KVPRY+R V  FP TVTG
Sbjct: 465 AVVGVPDDRMGEELCAWVRLRAGAQADAESIRDFCRGQIAHFKVPRYVRIVAEFPTTVTG 524

Query: 556 KIQKFKIRDEMKDQLG 571
           K+QKF IR+ M  +LG
Sbjct: 525 KVQKFLIREAMIAELG 540


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: 901
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: 554
Length adjustment: 36
Effective length of query: 542
Effective length of database: 518
Effective search space:   280756
Effective search space used:   280756
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 17 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