Alignments for a candidate for prpE in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Thiomicrospira cyclica ALM1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_013835422.1 THICY_RS04490 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000214825.1:WP_013835422.1
          Length = 651

 Score =  831 bits (2146), Expect = 0.0
 Identities = 402/656 (61%), Positives = 503/656 (76%), Gaps = 9/656 (1%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           IES++ E RVF P +    QAAI + +   A+  +AE+D+ GFWA  A+E L W KPFTK
Sbjct: 5   IESILTETRVFEPSDAIKQQAAIKA-DKLDAMYAKAEQDHVGFWADLAKEKLSWHKPFTK 63

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
            LD S AP Y+WF DGELN SYNC+DR+L    +DK+AI+FE D G V   TY+ELH +V
Sbjct: 64  ALDDSKAPLYRWFTDGELNVSYNCIDRHLDT-KSDKLAIIFEGDKGDVHHYTYQELHDEV 122

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
           CRFAN LK  GI++GDRV+IYMPM  + V+AMQACAR+GA HSVVFGGFSA++L++R+ +
Sbjct: 123 CRFANTLKTQGIKQGDRVIIYMPMIPQAVIAMQACARVGAIHSVVFGGFSAEALKDRVEN 182

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
             A  +IT D  +RGGKA+PLK   D ALA G C++V+ VIVY+RT  +V   +GRD W 
Sbjct: 183 AAAKLIITTDGGLRGGKAIPLKGAVDQALAKG-CDSVKKVIVYQRTKQEVVMQDGRDIWW 241

Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
            +  AG  +  +   + A+HPLF+LYTSGSTG PKGVQH +GGYLL A++T +W FD+  
Sbjct: 242 HEAEAGMSNYHDPVMLPADHPLFLLYTSGSTGTPKGVQHGSGGYLLNAMLTNEWMFDLND 301

Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
            D+FWCTAD+GW+TGH+Y+AYGPLA GAT V+FEGVPTYP+AGRFW +   H V++FYTA
Sbjct: 302 KDVFWCTADVGWITGHSYVAYGPLAMGATIVMFEGVPTYPDAGRFWQVCQDHGVTVFYTA 361

Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
           PTAIR+L+K      K  P QYDLS LR+LGTVGEPINPEAWMWY++ IG   CPI+DT+
Sbjct: 362 PTAIRALMKFG----KDIPAQYDLSKLRILGTVGEPINPEAWMWYHEVIGRGECPIIDTW 417

Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483
           WQTETG HMI P PG TPL PGSCT PLPGI A +VDE GH++ N +GG LVV++PWP+M
Sbjct: 418 WQTETGAHMIAPFPGVTPLKPGSCTRPLPGIDAIVVDEEGHEIGNNSGGYLVVRKPWPSM 477

Query: 484 IRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTM 543
           ++T+WGD +R+  +YF  +   + Y+ GD + +D D GY  I+GRIDDVLNVSGHR+GTM
Sbjct: 478 LQTVWGDDQRYIDTYF-AKFNNQYYVVGDSAHKDAD-GYIWILGRIDDVLNVSGHRLGTM 535

Query: 544 EIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEI 603
           EIESALV++P VAEAAVVG+P D+ GE++ AFVVL    P G E   +  ELRNWV +EI
Sbjct: 536 EIESALVAHPKVAEAAVVGKPHDVKGESVFAFVVLNTDLPAGAERDAMVNELRNWVAQEI 595

Query: 604 GPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659
           GPIAKP DIRFG NLPKTRSGKIMRRLLR++AKGEEITQDTSTLE+P+IL+QL+QA
Sbjct: 596 GPIAKPDDIRFGTNLPKTRSGKIMRRLLRTIAKGEEITQDTSTLEDPSILKQLQQA 651


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: 1304
Number of extensions: 64
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: 651
Length adjustment: 38
Effective length of query: 622
Effective length of database: 613
Effective search space:   381286
Effective search space used:   381286
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.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis