Alignments for a candidate for prpE in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Rhodomicrobium vannielii ATCC 17100

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_013419313.1 RVAN_RS08390 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000166055.1:WP_013419313.1
          Length = 648

 Score =  904 bits (2336), Expect = 0.0
 Identities = 421/627 (67%), Positives = 510/627 (81%), Gaps = 2/627 (0%)

Query: 19  INPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLA 78
           I+  +Y A+Y+QS++ P+ FWGEQ   +DWIKP+ KVKNTS+ P NVSIKWYEDG+LN+A
Sbjct: 18  IDENKYRALYEQSVSDPEGFWGEQAARIDWIKPFTKVKNTSYDPHNVSIKWYEDGSLNVA 77

Query: 79  ANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAIY 138
           ANC+DRHL+  GD+ AIIWEGD+ +    ++Y+ELH  V RFAN L + G+KKGD V IY
Sbjct: 78  ANCIDRHLETRGDQIAIIWEGDEPNLDLKVTYRELHDRVSRFANVLKKHGVKKGDRVTIY 137

Query: 139 MPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPL 198
           +PM+PEAA AMLACARIGA+HSV+FGGFSP+++A RI+D +S +VIT+DEGVR GR +PL
Sbjct: 138 LPMIPEAAYAMLACARIGAIHSVVFGGFSPDSLASRIVDCDSSVVITADEGVRGGRKVPL 197

Query: 199 KKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDP 258
           K N D AL+     SVE V+V+KRT G + W  GRD W  + +E  S     EE+NAEDP
Sbjct: 198 KANADKALEK--CPSVERVLVVKRTNGTVGWTPGRDYWLAEEMESVSADCPPEEINAEDP 255

Query: 259 LFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLY 318
           LFILYTSGSTG+PKGVLHT+GGYLVYA+LT +Y+FDY  GDIYWCTADVGWVTGHSY+LY
Sbjct: 256 LFILYTSGSTGQPKGVLHTSGGYLVYASLTHQYIFDYKDGDIYWCTADVGWVTGHSYILY 315

Query: 319 GPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRS 378
           GPLA GATT+MFEGVPN+PT +R   V+DKHQVN  YTAPTAIRALM  GD+ ++ T R 
Sbjct: 316 GPLANGATTVMFEGVPNYPTASRFWDVIDKHQVNTFYTAPTAIRALMGAGDELVKKTSRK 375

Query: 379 SLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSAT 438
           SL++LGSVGEPINPEAWEWY+  +G E+CP+VDTWWQTETGG +I+ LPGA  LK GSAT
Sbjct: 376 SLKLLGSVGEPINPEAWEWYYHVVGEERCPIVDTWWQTETGGILISALPGAIALKPGSAT 435

Query: 439 RPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFS 498
            PFFG++PALV  +G P+EGA EG+LVITDSWPGQ R+++ DH RF QTYFS +   YF+
Sbjct: 436 LPFFGIKPALVTPDGQPIEGAGEGNLVITDSWPGQMRSVYKDHTRFVQTYFSAYPGTYFT 495

Query: 499 GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQA 558
           GDG RRDEDGYYWITGRVDDV+NV+GHR+GTAE+ESALVAHPK+AEAA VG PH++KGQ 
Sbjct: 496 GDGCRRDEDGYYWITGRVDDVINVAGHRMGTAEVESALVAHPKVAEAACVGYPHSLKGQG 555

Query: 559 IYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKI 618
           IY YVTL  G EP+  L  E+RNWVR+EIGP+ATPD++ +   LPKTRSGKIMRRILRKI
Sbjct: 556 IYVYVTLMEGIEPTEALRTELRNWVRQEIGPIATPDLIQFAPGLPKTRSGKIMRRILRKI 615

Query: 619 AAGDTSNLGDTSTLADPGVVEKLLEEK 645
           A  D SNLGDTSTLA+PGVV  L+E +
Sbjct: 616 AEDDFSNLGDTSTLAEPGVVSDLIENR 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: 1482
Number of extensions: 58
Number of successful extensions: 2
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: 648
Length adjustment: 38
Effective length of query: 614
Effective length of database: 610
Effective search space:   374540
Effective search space used:   374540
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 Apr 09 2024. 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 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