Alignments for a candidate for prpE in Methylohalobius crimeensis 10Ki

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Methylohalobius crimeensis 10Ki

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_022948469.1 H035_RS0107990 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000421465.1:WP_022948469.1
          Length = 650

 Score =  847 bits (2187), Expect = 0.0
 Identities = 401/647 (61%), Positives = 492/647 (76%), Gaps = 7/647 (1%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQG-KILDWIKPYQKVKNTS 59
           MSQ   + +P  I  R  ++  +Y  +Y +S++ PD FW EQ  + + W +P++ V +  
Sbjct: 1   MSQAKIYPVPPEIETRAHMSADRYRRLYARSLSDPDGFWAEQAERFVSWDQPWKTVSDWD 60

Query: 60  FAPGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCR 119
           F    V I+W+E G LN   NCLDRHL+  GD TAIIWE DD + S+ +SY+ELH +VC+
Sbjct: 61  F--NRVHIRWFEGGRLNACFNCLDRHLESRGDETAIIWESDDPAHSRSLSYRELHEEVCK 118

Query: 120 FANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSN 179
           FAN L + G+ KGD V IY+PM+PEAAVAMLACARIGA+HSV+FGGFS +A+  RI D+ 
Sbjct: 119 FANVLKQHGVAKGDRVCIYLPMIPEAAVAMLACARIGAIHSVVFGGFSADALRDRIRDAE 178

Query: 180 SRLVITSDEGVRAGRSIPLKKNVDDALKN-PNVTSVEHVVVLKRTGGKIDWQEGRDLWWH 238
           +  +IT+D G+R G+ + LK N D AL   P VT   HV+V++R+G  + WQEGRD+W+H
Sbjct: 179 AHTLITADAGLRGGKHVSLKANADQALSQCPGVT---HVIVVRRSGTDVSWQEGRDIWYH 235

Query: 239 DLVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPG 298
           + +  A+ Q + E M+AEDPLFILYTSGSTGKPKGVLHTTGGYLVYA +T  YVFDYH G
Sbjct: 236 EAMASAAPQCEPEIMDAEDPLFILYTSGSTGKPKGVLHTTGGYLVYATMTHHYVFDYHEG 295

Query: 299 DIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAP 358
           ++YWCTADVGW+TGH+YL+YGPL  GA T+MFEGVP WP P R  QVVDKH+VNI YTAP
Sbjct: 296 EVYWCTADVGWITGHTYLVYGPLCNGAVTVMFEGVPMWPEPDRFWQVVDKHRVNIFYTAP 355

Query: 359 TAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTET 418
           TAIRALM  GD+ +  T R SLR+LGSVGEPINPEAWEWY + +G  +CPVVDTWWQTET
Sbjct: 356 TAIRALMRVGDEYVGRTSRRSLRLLGSVGEPINPEAWEWYHRVVGESRCPVVDTWWQTET 415

Query: 419 GGFMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLF 478
           GG +ITPLPGAT LK GSAT PFFG++P ++D++ N L+G+ EG L +  SWPGQARTL+
Sbjct: 416 GGILITPLPGATPLKPGSATLPFFGIEPVILDDKNNELQGSAEGILALKRSWPGQARTLY 475

Query: 479 GDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVA 538
            +HERF +TYF  F   YF+GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVA
Sbjct: 476 KNHERFVETYFKPFPGHYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVA 535

Query: 539 HPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHW 598
           HP +AEAAVVG PH+IKGQ IYAYV    G E  PEL   + + V +EIGP+A PD + +
Sbjct: 536 HPDVAEAAVVGYPHDIKGQGIYAYVIPKRGVETGPELAQSLVDLVNREIGPIAKPDAIQF 595

Query: 599 TDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
              LPKTRSGKIMRRILRKIA+     LGDTSTLADP V++ LLE +
Sbjct: 596 APDLPKTRSGKIMRRILRKIASQQIDQLGDTSTLADPSVIDHLLENR 642


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: 1435
Number of extensions: 55
Number of successful extensions: 3
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: 650
Length adjustment: 38
Effective length of query: 614
Effective length of database: 612
Effective search space:   375768
Effective search space used:   375768
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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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