Alignments for a candidate for aacS in Luteimonas huabeiensis HB2

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Luteimonas huabeiensis HB2

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_024890575.1 Z164_RS0110065 AMP-binding protein

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



>NCBI__GCF_000559025.1:WP_024890575.1
          Length = 569

 Score =  699 bits (1805), Expect = 0.0
 Identities = 348/566 (61%), Positives = 423/566 (74%), Gaps = 6/566 (1%)

Query: 8   TNSAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAH 67
           + +APL  SH RGA   PL+E+T+GA  A +    P+R ALV   QG R  +  L     
Sbjct: 2   SRTAPLATSHVRGADAPPLLEETVGALLARIARTWPDRPALVVPPQGVRMDWRALDRAVS 61

Query: 68  RLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKV 127
           RLA+ LL +GL+PGDRVGIWS N AEWVLMQ ATA+ GLVLVNINPAYR+ E+EYAL +V
Sbjct: 62  RLAAGLLALGLSPGDRVGIWSLNRAEWVLMQFATARAGLVLVNINPAYRSHELEYALTRV 121

Query: 128 GCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEP 187
           GC+ LV    FKTS YL MLRELAPE     PG L A +LP L+ V+ +    G+G D P
Sbjct: 122 GCRALVLARAFKTSRYLDMLRELAPELARAAPGLLFAERLPDLRHVLVL----GEGEDVP 177

Query: 188 GLLRFTELIARGNAA-DPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGF 246
           G  RF ++ A  +AA   RL  V  GL+   PINIQFTSGTTG PKGATLTHRNILNNG+
Sbjct: 178 GAWRFDDVAACDDAAAHARLRAVEPGLRPEQPINIQFTSGTTGSPKGATLTHRNILNNGW 237

Query: 247 FIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDER 306
           F+GE M+LT  DRLCIPVP YHCFGMVLGNLAC THG+ +V P +GFDP   L+TVQ ER
Sbjct: 238 FVGERMRLTEHDRLCIPVPFYHCFGMVLGNLACATHGSCMVVPGEGFDPQATLRTVQAER 297

Query: 307 CTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYG 366
           CT LHGVPTMFIA L  P F  ++LS+LRTGIMAGSPCP +VMKRVV +M++ E+TIAYG
Sbjct: 298 CTALHGVPTMFIAMLGLPDFDAYDLSSLRTGIMAGSPCPVDVMKRVVSRMHMSEVTIAYG 357

Query: 367 MTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVM 426
           MTETSPVS Q++ D PL +RV +VG++ PH+E K+VD D   V P G+ GE  T+GYSVM
Sbjct: 358 MTETSPVSFQTTPDDPLDRRVDSVGRIHPHVEAKLVDADGRTVAP-GETGELWTRGYSVM 416

Query: 427 HGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFL 486
            GYWG+  +T E +D  GWM TGDLAT+DA+GY  IVGR+KDM+IRGGEN+YPREIEEFL
Sbjct: 417 RGYWGEPQRTAEVLDADGWMRTGDLATLDADGYCRIVGRLKDMLIRGGENVYPREIEEFL 476

Query: 487 YRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFV 546
           + HP + DVQV GVPD ++GEE+CAWI    G Q  E+ +RAFC+G+IAHYKVPRY+RFV
Sbjct: 477 HGHPAIADVQVFGVPDARFGEEICAWIRLAEGAQLDEEAVRAFCRGRIAHYKVPRYVRFV 536

Query: 547 TSFPMTVTGKIQKFKIRDEMKDQLGL 572
            +FPMTV+GK QK+ +R+ M+ +LGL
Sbjct: 537 ETFPMTVSGKAQKYLMREAMRAELGL 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: 943
Number of extensions: 34
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: 569
Length adjustment: 36
Effective length of query: 542
Effective length of database: 533
Effective search space:   288886
Effective search space used:   288886
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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Candidates (tab-delimited)
Steps (tab-delimited)
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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