GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Azoarcus olearius BH72

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011766145.1 AZO_RS12180 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000061505.1:WP_011766145.1
          Length = 654

 Score = 1061 bits (2745), Expect = 0.0
 Identities = 500/649 (77%), Positives = 571/649 (87%)

Query: 9   QEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQS 68
           Q+ R++NP E     AA+  MEAY ALC EAE+DYEG+WAR+AREL+ W KPFT+VLD+S
Sbjct: 5   QQVRIYNPSEEVVKNAAVSGMEAYWALCKEAEQDYEGYWARNARELIDWKKPFTQVLDES 64

Query: 69  NAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFAN 128
           NAPF+KWF DG+LN SYNCLDRN++ G  DKVA++FEAD G VTRVTY++L G+VC+FAN
Sbjct: 65  NAPFFKWFADGQLNVSYNCLDRNVEKGLGDKVALIFEADSGEVTRVTYKDLLGRVCKFAN 124

Query: 129 GLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVA 188
            L+A GI+KGDRVVIY+PMS+EGVVAMQACAR+GATHS+VFGGFSA++L++R+ D GAVA
Sbjct: 125 ALRASGIKKGDRVVIYLPMSIEGVVAMQACARIGATHSIVFGGFSAQALRDRINDAGAVA 184

Query: 189 LITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSA 248
           LIT+D Q RGGKALPLK IAD+AL+LGGCE ++NV V +RTG  VA+  GRD W  DV A
Sbjct: 185 LITSDGQFRGGKALPLKPIADEALSLGGCETIKNVFVVKRTGADVAFVAGRDVWYHDVVA 244

Query: 249 GQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFW 308
            Q D CE E V AEHPLF+LYTSGSTGKPKGVQHSTGGYLL A++TMK+TFDIKP D+FW
Sbjct: 245 SQSDVCEPEWVDAEHPLFLLYTSGSTGKPKGVQHSTGGYLLHAILTMKYTFDIKPSDVFW 304

Query: 309 CTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIR 368
           CTADIGWVTGHTYI YGPLA G+T++VFEGVPTYP+AGRFW MI  HKV+IFYTAPTAIR
Sbjct: 305 CTADIGWVTGHTYITYGPLACGSTEIVFEGVPTYPDAGRFWKMIQDHKVNIFYTAPTAIR 364

Query: 369 SLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTET 428
           SLIKAA+ +  +HPK YDLSSLR+LG+VGEPINP AW WYY+N+G  RCPIVDTFWQTET
Sbjct: 365 SLIKAADNNPTVHPKNYDLSSLRILGSVGEPINPAAWEWYYENVGGGRCPIVDTFWQTET 424

Query: 429 GGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIW 488
           GGHMITPLPGATPLVPGSCTLP PGI AA+VDETG +VPNG GGILVVKRPWP+MIRTIW
Sbjct: 425 GGHMITPLPGATPLVPGSCTLPFPGIQAAVVDETGTEVPNGQGGILVVKRPWPSMIRTIW 484

Query: 489 GDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESA 548
           GDPERF+KSY+P++  GKLYLAGDG+IRDK+TGYFTI GRIDDVLNVSGHRMGTMEIESA
Sbjct: 485 GDPERFKKSYYPDDFKGKLYLAGDGAIRDKETGYFTITGRIDDVLNVSGHRMGTMEIESA 544

Query: 549 LVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAK 608
           LV++  VAEAAVVGRPDD+TGEAI AFVVLK +RPTGE A  +  EL+NWVG EIGPIAK
Sbjct: 545 LVAHEKVAEAAVVGRPDDLTGEAIVAFVVLKGARPTGEAAAAVVKELQNWVGHEIGPIAK 604

Query: 609 PKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657
           PKDIRFG+NLPKTRSGKIMRRLLR LAKGEEITQDTSTLENPAILEQLK
Sbjct: 605 PKDIRFGENLPKTRSGKIMRRLLRQLAKGEEITQDTSTLENPAILEQLK 653


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: 1528
Number of extensions: 63
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: 660
Length of database: 654
Length adjustment: 38
Effective length of query: 622
Effective length of database: 616
Effective search space:   383152
Effective search space used:   383152
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

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:

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:

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:

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:

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