Alignments for a candidate for prpE in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Paraburkholderia bryophila 376MFSha3.1

Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate H281DRAFT_05523 H281DRAFT_05523 propionyl-CoA synthetase (EC 6.2.1.17)

Query= metacyc::MONOMER-21334
         (629 letters)



>FitnessBrowser__Burk376:H281DRAFT_05523
          Length = 648

 Score =  648 bits (1671), Expect = 0.0
 Identities = 318/633 (50%), Positives = 435/633 (68%), Gaps = 20/633 (3%)

Query: 8   ESWKSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDRHVEAGRG 67
           E W++DP AFW  AA S+ W       L       + WF  A  N  +N +DRHVEAGRG
Sbjct: 8   EDWRTDPMAFWARAASSVAWSRPWDEVLTHQPGQRFSWFDGAYTNASYNCLDRHVEAGRG 67

Query: 68  EQTAIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIPEALEAML 127
           EQ AI ++SP+T T + ++Y  LR++VA  AG L+ +GV  GD V+IYMP+IP+A+ AML
Sbjct: 68  EQVAIAFESPVTGTAQTLTYASLRDQVAGFAGVLQLQGVRMGDVVVIYMPVIPQAIIAML 127

Query: 128 ACARLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLDGAIDMAK 187
           ACAR+GA H VVFGGFAA+ELA R+ D  P+ I+ ASCG E  R + YK  +D A+  + 
Sbjct: 128 ACARIGATHCVVFGGFAASELAKRLRDTLPRVIVTASCGFEVKRRIPYKETVDEAVLQSA 187

Query: 188 HKPEFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTSGTTGAPK 247
            +    +++QRE     L E RD +W     G      +PV   HP YIL+TSGTTG+PK
Sbjct: 188 WQGPV-IVYQRELGRVELAE-RDVDWERAMCGTYGVSPIPVPAGHPLYILHTSGTTGSPK 245

Query: 248 GVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTTIVFEG 307
           G+ R T G++ AL W+M NIY   PGDVFWAASD+GWVVGHSY+ YGPL++G TT++FEG
Sbjct: 246 GIQRDTGGYMTALLWSMNNIYRSLPGDVFWAASDIGWVVGHSYMTYGPLLNGCTTVLFEG 305

Query: 308 KPVGTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDP---------KGEMLAKYDLSHL 358
           KPVGTPDA  FWRVI++H+V   FTAPTA+RA+K+EDP          GE+  +YDL  L
Sbjct: 306 KPVGTPDAAAFWRVIAKHRVNVLFTAPTALRAIKKEDPGGYQLREPVMGELHWRYDLGSL 365

Query: 359 KALYLAGERADPDTIIWAQKALSVPVIDHWWQTETGWTIAGNP----LGIEELPTKLGSP 414
           ++++LAGER D  TI WA+  L VPV+DHWWQTE GW +A +     LG E    + G+ 
Sbjct: 366 RSVFLAGERCDTTTIEWAEDLLHVPVLDHWWQTEAGWPMAASTAKGALGGER---RRGAA 422

Query: 415 AKAMPGYDVQILDEGGHQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYY 474
            +A+PG+DV+ +D+ G ++  G  G +   LPLPPG +  +WNA  R+ +SY   FPG+Y
Sbjct: 423 GRALPGWDVRCVDDQGAEVDAGASGNVVCGLPLPPGAMTTIWNAHERYERSYFGRFPGWY 482

Query: 475 ETGDAGMIDEDGYLYIMARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKG 534
           +TGDAG +D DG++++M RTDDVINVAGHRLSTG +EE+++  + VAECAV+G++  LKG
Sbjct: 483 DTGDAGYVDADGFVFVMGRTDDVINVAGHRLSTGAIEEIVSRLDAVAECAVVGMAHPLKG 542

Query: 535 QMPLGFLCLNNGCNRDHGDVVK-EVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGT 593
           Q+PL FL L +G ++D  D  +   VK+VR+++G VA+ + A VV+RLPKTRSGKILR +
Sbjct: 543 QVPLVFLVLKDG-SKDGADAAETAAVKVVREQLGAVASMQAAFVVERLPKTRSGKILRRS 601

Query: 594 MVSIADGKEYKMPATIDDPAILDEIKVALQSLG 626
           ++ I DGK   +PATI+DP +L +++  +++ G
Sbjct: 602 LLQIVDGKAVAIPATIEDPGVLVDVERIVKARG 634


Lambda     K      H
   0.319    0.137    0.428 

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: 1331
Number of extensions: 64
Number of successful extensions: 4
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: 629
Length of database: 648
Length adjustment: 38
Effective length of query: 591
Effective length of database: 610
Effective search space:   360510
Effective search space used:   360510
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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