Alignments for a candidate for prpE in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Halomonas desiderata SP1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_086512010.1 BZY95_RS21920 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_002151265.1:WP_086512010.1
          Length = 649

 Score =  948 bits (2450), Expect = 0.0
 Identities = 442/634 (69%), Positives = 527/634 (83%)

Query: 12  NIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYE 71
           +IA    I+ ++Y+AMYQQS++ P+ FW EQ K +DW K   K+K+TSF P NV I+W+E
Sbjct: 13  DIAANAWIDREKYQAMYQQSVDDPEGFWAEQAKRIDWFKAPTKIKHTSFDPHNVDIRWFE 72

Query: 72  DGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKK 131
           DGTLN + +CLDRHL++ GD+TAIIWEGDD   SKH+SY+ELH   C+ AN L ELGI K
Sbjct: 73  DGTLNASVSCLDRHLEKRGDQTAIIWEGDDPKDSKHVSYRELHAKTCQLANALKELGIGK 132

Query: 132 GDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVR 191
           GDVV +YMPM+PEAAVAMLACARIGAVHSV+FGGFSP+A+A RI+ ++SRLVIT+DE VR
Sbjct: 133 GDVVTLYMPMIPEAAVAMLACARIGAVHSVVFGGFSPDALAQRIVGADSRLVITADESVR 192

Query: 192 AGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAE 251
            G+ +PLK NVD AL        E V+V+KRTGG I+W+EGRD+W+HDLV++ S    AE
Sbjct: 193 GGKHVPLKDNVDAALTRKGTEVCEKVLVVKRTGGDIEWKEGRDVWYHDLVDKQSADCPAE 252

Query: 252 EMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVT 311
           EMNAEDPLFILYTSGSTG PKG+ HTTGGYLVYA+LT +Y+FDY  G++YWCTADVGWVT
Sbjct: 253 EMNAEDPLFILYTSGSTGAPKGLKHTTGGYLVYASLTHQYIFDYQDGEVYWCTADVGWVT 312

Query: 312 GHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKA 371
           GHSY++YGPLA GATTLMFEGVP++P+  RM +VVDKH V ILYTAPTAIRALMA GD  
Sbjct: 313 GHSYIVYGPLANGATTLMFEGVPSYPSHGRMGEVVDKHNVAILYTAPTAIRALMAHGDGV 372

Query: 372 IEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATE 431
           ++ + R SLR+LGSVGEPINPEAWEWY + IGN KCP+VDTWWQTETGG MI PLPGA +
Sbjct: 373 MDSSKRDSLRLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGGIMIAPLPGAMD 432

Query: 432 LKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFST 491
           LK GSAT PFFGVQPAL+D+EGN L+GA +G+LVI+DSWPGQAR+++GDH+RF QTYFST
Sbjct: 433 LKPGSATLPFFGVQPALLDSEGNELQGAVDGNLVISDSWPGQARSIWGDHDRFIQTYFST 492

Query: 492 FKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIP 551
           +K  YF+GDG RRDEDGYYWITGRVDDVLNVSGHR+GTAEIES+LVAH  +AEAAVVG P
Sbjct: 493 YKGYYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRMGTAEIESSLVAHEAVAEAAVVGFP 552

Query: 552 HNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIM 611
           H+IKGQ IY YVTL  G EP+ EL  E+  WVRK+IGP+A+PDV+ W   LPKTRSGKIM
Sbjct: 553 HDIKGQGIYIYVTLGDGVEPTDELKKELTQWVRKDIGPIASPDVIQWAPGLPKTRSGKIM 612

Query: 612 RRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           RRILRKIAA +T  LGDTSTLADP VV+ L+E +
Sbjct: 613 RRILRKIAANETDGLGDTSTLADPSVVDDLIENR 646


Lambda     K      H
   0.317    0.135    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: 1501
Number of extensions: 51
Number of successful extensions: 1
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: 652
Length of database: 649
Length adjustment: 38
Effective length of query: 614
Effective length of database: 611
Effective search space:   375154
Effective search space used:   375154
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 Sep 24 2021. 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)
SQLite3 databases

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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 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