Alignments for a candidate for prpE in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Cereibacter sphaeroides ATCC 17029

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011841528.1 RSPH17029_RS11250 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000015985.1:WP_011841528.1
          Length = 653

 Score =  836 bits (2159), Expect = 0.0
 Identities = 400/643 (62%), Positives = 496/643 (77%), Gaps = 5/643 (0%)

Query: 7   HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66
           +T  A+   +  ++   YE MY  S+  P+ FWGEQGK LDWIKPY KVKNT+F PG VS
Sbjct: 10  YTASADFIAQAHVDAAGYERMYAASVADPEAFWGEQGKRLDWIKPYTKVKNTNFRPGEVS 69

Query: 67  IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQ-SKHISYKELHRDVCRFANTLL 125
           IKW+EDGTLN+A NC+DRHL     +TAIIWE DD +  ++HISY+ELH +VCR AN L+
Sbjct: 70  IKWFEDGTLNIAWNCIDRHLATRAKQTAIIWEPDDPNAPAQHISYQELHDNVCRMANVLV 129

Query: 126 ELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVIT 185
             G++KGD V +Y+PM+PEAA AMLACARIGA+HSV+F GFSP+A+A RI D  +++VIT
Sbjct: 130 SQGVRKGDRVVMYLPMIPEAAYAMLACARIGAIHSVVFAGFSPDALANRINDCQAKVVIT 189

Query: 186 SDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQAS 245
           +D   R GR  PLK N D AL +   +     +V+K TG +I W +GRD+   +L+  AS
Sbjct: 190 ADTAPRGGRRTPLKSNTDAALLH--CSDRVRCLVVKHTGDQIHWMDGRDVDVKELMRHAS 247

Query: 246 DQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTA 305
                EE+NAEDPLFILYTSGSTGKPKGV+HT+GGYL YAA+T +  FDYH GD++WCTA
Sbjct: 248 PDCPIEEVNAEDPLFILYTSGSTGKPKGVVHTSGGYLTYAAMTHQMTFDYHDGDVFWCTA 307

Query: 306 DVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALM 365
           DVGWVTGHSY++YGPLA GATTLMFEGVP +P   R   V +KH+VN  YTAPTAIR+LM
Sbjct: 308 DVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDAGRFWAVCEKHKVNQFYTAPTAIRSLM 367

Query: 366 AEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITP 425
             G + ++  D SSL++LGSVGEPINPEAW WY   +G  +CP+VDT+WQTETGG MITP
Sbjct: 368 GLGPEWVDKYDLSSLKLLGSVGEPINPEAWSWYNTHVGKGRCPIVDTFWQTETGGHMITP 427

Query: 426 LPGATELKAGSATRPFFGVQPALVD-NEGNPL-EGATEGSLVITDSWPGQARTLFGDHER 483
           LPGA  +K G+A++PFFGV+P ++D  +G+ L E ATEG L I DSWPGQ RTL+GDHER
Sbjct: 428 LPGAIPVKPGAASKPFFGVKPVILDPTDGHELHETATEGVLCIADSWPGQMRTLWGDHER 487

Query: 484 FEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIA 543
           FE+ YFS +K  YF+GDG RRD DGYYW+TGRVDDV+NVSGHR+GTAE+ESALVAH ++A
Sbjct: 488 FEEAYFSQYKGYYFTGDGCRRDADGYYWVTGRVDDVINVSGHRMGTAEVESALVAHAQVA 547

Query: 544 EAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLP 603
           EAAVVG PH+IKGQ IYAYVTL +G +P+ EL  ++  WVR EIGP+A+PDV+ W   LP
Sbjct: 548 EAAVVGYPHDIKGQGIYAYVTLMNGVQPTEELRKDLVKWVRTEIGPIASPDVIQWAPGLP 607

Query: 604 KTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           KTRSGKIMRRILRKIA  D  +LGDT+TLADP VV+ L+  ++
Sbjct: 608 KTRSGKIMRRILRKIAENDFGSLGDTTTLADPSVVDDLIANRK 650


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: 1481
Number of extensions: 63
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: 652
Length of database: 653
Length adjustment: 38
Effective length of query: 614
Effective length of database: 615
Effective search space:   377610
Effective search space used:   377610
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 10 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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