GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Halioglobus japonicus S1-36

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_084200888.1 C0029_RS18225 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_002869505.1:WP_084200888.1
          Length = 643

 Score =  819 bits (2115), Expect = 0.0
 Identities = 398/647 (61%), Positives = 484/647 (74%), Gaps = 8/647 (1%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTS 59
           MS+   H +PAN  D   I+   Y+AMYQ+SI+ PD F+ +     L W +P+ KV    
Sbjct: 1   MSEFPTHPVPANFKD-AHIDADTYKAMYQRSIDDPDGFFSQMANDFLSWDQPWDKVMEYD 59

Query: 60  FAPGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCR 119
           F  G  +  W+  G LN++ NC+DRHL E  D+TA+IWEGDD + SKHI+Y EL   VC+
Sbjct: 60  FIKGEAA--WFAGGKLNVSYNCVDRHLPERADQTALIWEGDDPADSKHITYAELKDHVCK 117

Query: 120 FANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSN 179
            AN L   G+KKGD V IYMPM+PEAA AMLAC RIGAVHS++FGGFSPEA+  RI+DS+
Sbjct: 118 LANALKARGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSIVFGGFSPEALKDRILDSD 177

Query: 180 SRLVITSDEGVRAGRSIPLKKNVDDALKN-PNVTSVEHVVVLKRTGGKIDWQEGRDLWWH 238
            + VIT+DEGVR GR +PLK N D AL+  PNV +    +V++RT G + W   RD+W+H
Sbjct: 178 CQTVITADEGVRGGRKVPLKVNADKALEACPNVHTC---LVVERTSGDVAWNADRDVWYH 234

Query: 239 DLVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPG 298
           +LV+  S   + E M+AEDPLFILYTSGSTGKPKGVLHTTGGYL+ AA+TFKYVFDY  G
Sbjct: 235 ELVDGQSTDCEPESMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDG 294

Query: 299 DIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAP 358
           +IYWCTADVGWVTGH+Y++YGPLA GA +LMFEGVP +P   R  +VVDKHQVN  YTAP
Sbjct: 295 EIYWCTADVGWVTGHTYIVYGPLANGAISLMFEGVPTYPDAGRCWEVVDKHQVNTFYTAP 354

Query: 359 TAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTET 418
           TAIRAL A GD+ +    R SLR+LG+VGEPINPEAWEWY + +G+ +CP++DTWWQTET
Sbjct: 355 TAIRALQAVGDEPVTRASRVSLRLLGTVGEPINPEAWEWYHRVVGDGRCPIIDTWWQTET 414

Query: 419 GGFMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLF 478
           G  MITPLPGA  LK GSAT PFFGV+ AL++ +G+ +EG   G LV+  SWP Q RT+F
Sbjct: 415 GAHMITPLPGAVPLKPGSATFPFFGVELALLNEDGSEIEGPGAGYLVVKRSWPSQIRTVF 474

Query: 479 GDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVA 538
           GDH+R   TYF  +   YF+GDGA RDEDGYYWITGRVDDVLNVSGHR+GTAE+ESALV 
Sbjct: 475 GDHKRLIDTYFRNYPGYYFTGDGATRDEDGYYWITGRVDDVLNVSGHRMGTAEVESALVL 534

Query: 539 HPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHW 598
           H +IAEAAVVG PH+IKGQ IYAYVT   G EP+ EL  E+     KEIGP+A PD++ W
Sbjct: 535 HEEIAEAAVVGFPHDIKGQGIYAYVTPMQGVEPNEELRQELIALCVKEIGPIAKPDIIQW 594

Query: 599 TDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
              LPKTRSGKIMRRILRKIA  +  +LGDTSTLADP VV+ L+  +
Sbjct: 595 APGLPKTRSGKIMRRILRKIAENELDSLGDTSTLADPSVVDNLVANR 641


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: 1416
Number of extensions: 60
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: 643
Length adjustment: 38
Effective length of query: 614
Effective length of database: 605
Effective search space:   371470
Effective search space used:   371470
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.

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