GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Bacteroides thetaiotaomicron VPI-5482

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 352309 BT2782 long-chain-fatty-acid--CoA ligase (NCBI ptt file)

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



>FitnessBrowser__Btheta:352309
          Length = 549

 Score =  483 bits (1244), Expect = e-141
 Identities = 241/540 (44%), Positives = 343/540 (63%), Gaps = 8/540 (1%)

Query: 26  LIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVG 85
           L E+T+G +        P++E +V   +  R+T++QL      +A  L+ +G+  G  VG
Sbjct: 3   LFERTLGQWLEHWAEETPDKEYIVYSDRNLRFTWSQLNQRVDDMAKGLIAVGVERGTHVG 62

Query: 86  IWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLG 145
           IW+ N  +W+ +  A A++G V V +N  Y+ AE+EY         L  +   K SD++ 
Sbjct: 63  IWAANVPDWLTLLYACAKIGAVYVTVNTNYKQAELEYLCQNSDMHTLCIVNGEKDSDFVQ 122

Query: 146 MLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGN-AADP 204
           M   + PE +  + GHL++ + P +K V+++  E  +G     +    E++  GN   D 
Sbjct: 123 MTYTMLPELKTCERGHLKSERFPYMKNVIYVGQEKHRG-----MYNTAEILLLGNNVEDD 177

Query: 205 RLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPV 264
           RL ++ + +   D +N+Q+TSGTTGFPKG  LTH NI NNGF  GE MK T  D+LC  V
Sbjct: 178 RLTELKSKVDCHDVVNMQYTSGTTGFPKGVMLTHYNIANNGFLTGEHMKFTADDKLCCCV 237

Query: 265 PLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHP 324
           PL+HCFG+VL  + C THG T V   + FDPL VL ++  ERCT L+GVPTMFIAEL HP
Sbjct: 238 PLFHCFGVVLATMNCLTHGCTQVMV-ERFDPLVVLASIHKERCTALYGVPTMFIAELHHP 296

Query: 325 RFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS 384
            F  F++S LRTGIMAGS CP E+MK+V E+M ++ +T  YG+TE +P    +  D    
Sbjct: 297 MFDLFDMSCLRTGIMAGSLCPVELMKQVEEKMYMK-VTSVYGLTEAAPGMTATRIDDSFD 355

Query: 385 KRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGG 444
            R +TVG+     EV+++DP+TG   P+G +GE C +GY+ M GY+ +   T E ID+  
Sbjct: 356 VRCNTVGRDFEFTEVRVIDPETGEECPVGVQGEMCNRGYNTMKGYYKNPEATAEVIDKDN 415

Query: 445 WMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQK 504
           ++H+GDL   D +G   I GRIKDM+IRGGENIYPREIEEFLY+   V+DVQV G+P +K
Sbjct: 416 FLHSGDLGIKDEDGNYRITGRIKDMIIRGGENIYPREIEEFLYKLDGVKDVQVAGIPSKK 475

Query: 505 YGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           YGE + A+II + G +  E D+R FCK +I+ YK+P+Y+ FV  FPMT +GKIQKF+++D
Sbjct: 476 YGEAVGAFIILQEGVEMHESDVRDFCKNKISRYKIPKYVFFVKEFPMTGSGKIQKFRLKD 535


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: 791
Number of extensions: 30
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: 578
Length of database: 549
Length adjustment: 36
Effective length of query: 542
Effective length of database: 513
Effective search space:   278046
Effective search space used:   278046
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