Alignments for a candidate for prpE in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Pseudarthrobacter sulfonivorans Ar51

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_058930181.1 AU252_RS07515 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_001484605.1:WP_058930181.1
          Length = 738

 Score =  545 bits (1405), Expect = e-159
 Identities = 310/674 (45%), Positives = 405/674 (60%), Gaps = 41/674 (6%)

Query: 8   MQEHRVFNPPEG----FASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP--- 60
           +Q+  V   P G      S  +  +   + A  + A+ D   FW + A  L  W +P   
Sbjct: 60  LQDVAVHGAPSGGPARHGSTTSSTTAAQHTAEHEAAQPDNVAFWEQQALRL-DWAQPAGI 118

Query: 61  ---------FTKVLDQSNA---PFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADD 108
                      +V   + A   P   WFE G+LN +YNC+DR++ NG  D VA  FE + 
Sbjct: 119 SGGKPWHTAHRRVPADAAAGKGPEITWFEGGKLNVAYNCVDRHVANGRGDNVAFHFEGEP 178

Query: 109 GSVTRVTYRELHGKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVV 168
           G    VTY EL  +V + AN L ALGI KGDRVVIY+P+  E V+   A AR+GA HS+V
Sbjct: 179 GDRRTVTYAELQREVSKAANALLALGITKGDRVVIYLPVIPETVIITLAVARIGAIHSLV 238

Query: 169 FGGFSAKSLQERLVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRR 228
           FGGFSA +L+ R+ D GA  L+T D Q R G A+P+K  AD A+A  G  A+ +V+V  R
Sbjct: 239 FGGFSADALKFRVEDTGAKLLVTTDGQFRRGVAVPVKDNADAAVA--GDNAIEHVLVVNR 296

Query: 229 TGGK-----VAWTEGRDRWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHS 283
           T        V  TEGRD W  D      D  E E   AE PLF++YTSG+TGKPKG+ H+
Sbjct: 297 TTAPEDLAAVPMTEGRDVWWHDAVGSAADVHEPEAFDAETPLFIMYTSGTTGKPKGLVHT 356

Query: 284 TGGYLLWALMTMKWTFD-----IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEG 338
           +GGYL  A  + +  F      ++  D+ WCTAD+ WVT HTY  YGPL+ GATQV+FEG
Sbjct: 357 SGGYLTQASWSFEHLFSNPDPALRDQDVHWCTADLAWVTAHTYEIYGPLSNGATQVIFEG 416

Query: 339 VPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGE 398
            P  P+ GR +++I R+ V+ +YTAPT +RSL+          P  YDLSS+RLLGTVGE
Sbjct: 417 TPNTPHPGRHFEIIERYGVTQYYTAPTLVRSLMGWFPDGV---PDSYDLSSIRLLGTVGE 473

Query: 399 PINPEAWMWYYKNIGNERCPIVDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAI 458
            +NPEAW W  +N+G    P+VDT+WQ+ETG  +++P P  T   PG    PLPG+   I
Sbjct: 474 AVNPEAWRWLRQNVGAGTAPVVDTWWQSETGATILSPAPTDTEFKPGCAARPLPGVSTRI 533

Query: 459 VDETGHDVPNGNGGILVVKRPWPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDK 518
           VD+ G+ VP G  G +VV  P PA+ RT+WG+P R+  +Y+ + +    +LAGDG+  D 
Sbjct: 534 VDDAGNTVPPGVQGFIVVDTPGPAIARTVWGNPRRYYDAYWSKYVEQGWFLAGDGAKYDA 593

Query: 519 DTGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVL 578
           D G   I+GR+DD LNVSGH + T+EIESALVS+  V EA V    D  TG AI AFVVL
Sbjct: 594 D-GDIWILGRVDDTLNVSGHLLSTIEIESALVSHADVVEAGVCPVADPTTGHAIVAFVVL 652

Query: 579 KRSRPTGEEAVKIATELRNWVGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGE 638
           KR       + ++ATELRN V K IGPIAKP+D+    ++PKTRSGKIMRRLL  L +G 
Sbjct: 653 KRG-----VSREVATELRNHVAKAIGPIAKPRDVVVVPDVPKTRSGKIMRRLLTQLFEGT 707

Query: 639 EITQDTSTLENPAI 652
            +   TS    PAI
Sbjct: 708 ALGDTTSLQNEPAI 721


Lambda     K      H
   0.319    0.136    0.422 

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: 1460
Number of extensions: 83
Number of successful extensions: 6
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: 660
Length of database: 738
Length adjustment: 39
Effective length of query: 621
Effective length of database: 699
Effective search space:   434079
Effective search space used:   434079
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 (21.7 bits)
S2: 54 (25.4 bits)

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

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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