Alignments for a candidate for aacS in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Tistlia consotensis USBA 355

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_085124878.1 B9O00_RS21920 AMP-binding protein

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



>NCBI__GCF_900177295.1:WP_085124878.1
          Length = 561

 Score =  543 bits (1400), Expect = e-159
 Identities = 271/565 (47%), Positives = 358/565 (63%), Gaps = 21/565 (3%)

Query: 2   TSSAAATNSAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQ 61
           T+     +  P   S   G +D PL++ TIG        R   R+A+VSV Q +  +YA 
Sbjct: 5   TTPGTEPDRKPPAPSCVAGPSDGPLLDTTIGQALRLTTERHGGRDAIVSVFQRQALSYAG 64

Query: 62  LQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVE 121
           L   A  +A ALL  G+ PGDRV IWS N  EW++      ++G ++V +NPA+R  E+ 
Sbjct: 65  LDLAADLVAGALLARGIRPGDRVAIWSANRIEWLIAHHGAVRIGAIVVTVNPAFRNEELA 124

Query: 122 YALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAG 181
           Y L   G +LL +   F++  +   +  + P             +LP L+TVV   D+A 
Sbjct: 125 YILEDSGARLLFAAPGFRSFSFTAAVAAVRP-------------RLPALETVVVFGDDAP 171

Query: 182 QGADEPGLLRFTELIARGNAADPRLAQVA-AGLQATDPINIQFTSGTTGFPKGATLTHRN 240
           +G +      +T  + R   ADP   + A A + A DP ++Q+TSGTTG PKGA LTHRN
Sbjct: 172 EGMES-----WTGFLDRD--ADPAAVRAAEAAVAADDPCSLQYTSGTTGRPKGALLTHRN 224

Query: 241 ILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQ 300
           ILNNG+F+G    L P DR+C+PVP +HCFG+VLG LA   HG+ +V P + FDP+  L 
Sbjct: 225 ILNNGYFVGLRQHLGPKDRICLPVPFFHCFGVVLGGLAALVHGSALVLPGESFDPIETLA 284

Query: 301 TVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLRE 360
            +  ERCT L+GVP MFIA   HP F   +LSTLRTG M  +PCP + M   VE+M++R+
Sbjct: 285 AIAAERCTALYGVPMMFIALQGHPEFGRHDLSTLRTGCMGAAPCPLKTMTDAVERMHMRQ 344

Query: 361 ITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCT 420
           IT+ YGMTETSP+S QS +   L  R+STVG +QPHLE K+VDP TG  V  GQRGE C 
Sbjct: 345 ITVVYGMTETSPISFQSLSSDDLETRISTVGAIQPHLEAKVVDPVTGRTVERGQRGELCV 404

Query: 421 KGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPR 480
           +GYSVM GYW     T EAID  GWMH+GDLA MD  GYV IVGR+KD +IRGGEN+YPR
Sbjct: 405 RGYSVMRGYWQRPEATAEAIDAEGWMHSGDLAVMDGRGYVQIVGRLKDTIIRGGENVYPR 464

Query: 481 EIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVP 540
           EIEEFL     V +  V G+PD++YGEE+CAWI  +PG +   + +R  C+G+IA YK+P
Sbjct: 465 EIEEFLLTLAPVAEAYVFGLPDERYGEEVCAWIRLRPGAETDAEALRELCRGRIATYKIP 524

Query: 541 RYIRFVTSFPMTVTGKIQKFKIRDE 565
           R IRFV +FP T +GK+QKF++R+E
Sbjct: 525 RSIRFVEAFPATASGKVQKFRMREE 549


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: 826
Number of extensions: 28
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: 561
Length adjustment: 36
Effective length of query: 542
Effective length of database: 525
Effective search space:   284550
Effective search space used:   284550
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources