Alignments for a candidate for acs in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Derxia gummosa DSM 723

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_084545335.1 H566_RS0120475 AMP-binding protein

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_000482785.1:WP_084545335.1
          Length = 662

 Score =  644 bits (1660), Expect = 0.0
 Identities = 320/612 (52%), Positives = 413/612 (67%), Gaps = 2/612 (0%)

Query: 64  ASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQGD 123
           A+ A+P  FW + A  I W +PW   L+    P   WF  G LN C+NA+DRH+  G G 
Sbjct: 43  AARANPAAFWAERAAAIDWLRPWDAALDASRAPFNRWFPGGQLNTCFNALDRHVLAGHGA 102

Query: 124 KIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAMLA 183
           + A+I+DS        +SY E+L + ++ AGVL   GV +GD VVIYMPM+ +A+ AMLA
Sbjct: 103 RTALIHDSAYDGRATRVSYAELLARTARFAGVLRDLGVGRGDRVVIYMPMVVEAVVAMLA 162

Query: 184 CARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQH 243
           CAR+GA+HS++FGGFA+ EL+TRID   PK VVTAS GIEPGR VEY PLL+ AL   +H
Sbjct: 163 CARLGAVHSVVFGGFAAPELATRIDDCTPKAVVTASCGIEPGRVVEYKPLLDAALARARH 222

Query: 244 KPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPK 303
               +++  RP      +  GRD DW+   A+A   DCVPV +  PLYILYTSGTTG PK
Sbjct: 223 AVPAVVVLQRPQCAAA-MTPGRDHDWQALDARATPADCVPVEATDPLYILYTSGTTGQPK 281

Query: 304 GVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEG 363
           G+VR  GG+AV L W++ ++Y + PG+V+WAASD+GW VGHSYI YGPLL G T +LYEG
Sbjct: 282 GIVRDNGGHAVALLWSVKAVYDIDPGDVFWAASDIGWQVGHSYITYGPLLAGATALLYEG 341

Query: 364 KPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGER 423
           KPVGTPDAGA++RVL EH V  L TAPTAIRAIR++DP  AL +   L  F+ LF+AGER
Sbjct: 342 KPVGTPDAGAFWRVLREHRVKVLLTAPTAIRAIRREDPDGALLRGLDLPDFRALFLAGER 401

Query: 424 CDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPGYNVMIL 483
            D +TL W++   RVPV+DHWWQTETG PI A  +G+        G   + VPG+++  L
Sbjct: 402 SDADTLRWAETHLRVPVVDHWWQTETGWPIAADPLGIERLPV-KHGSPTRAVPGWDIHAL 460

Query: 484 DDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEEG 543
           D + +++     G + V+LPLPPGA + +W   E F+  YF   PG+Y T DAG +D +G
Sbjct: 461 DADGREVAPGETGLLAVRLPLPPGAATTIWNADERFERAYFRDLPGWYKTGDAGCIDADG 520

Query: 544 YLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLALCVLKKD 603
           Y++VMSRVDDVINVAGHR+S GAIEE + +H  V +CAV+G  D LKG VP+   VLKK 
Sbjct: 521 YIFVMSRVDDVINVAGHRLSTGAIEEVLAAHPDVAECAVIGMADALKGQVPVGFVVLKKG 580

Query: 604 VNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNGKPYKVT 663
           V      V  E+V  VR  IGPVAAFR A+ V++LPKTRSGKI R+T++ + +GK   V 
Sbjct: 581 VARAHAAVAAEVVAAVRDRIGPVAAFRQALVVERLPKTRSGKILRATMAGIADGKEVAVP 640

Query: 664 PTIEDPSIFGHI 675
            TIED  +   I
Sbjct: 641 ATIEDAGVLEEI 652


Lambda     K      H
   0.318    0.136    0.421 

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: 1324
Number of extensions: 58
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: 683
Length of database: 662
Length adjustment: 39
Effective length of query: 644
Effective length of database: 623
Effective search space:   401212
Effective search space used:   401212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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