Aligments for a candidate for acs in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Paraburkholderia bryophila 376MFSha3.1

Align Acyl-CoA synthetase short-chain family member 3, mitochondrial; Acetate--CoA ligase 3; Acyl-CoA synthetase short-chain family member 3; Propionate--CoA ligase; EC 6.2.1.1; EC 6.2.1.17 (characterized)
to candidate H281DRAFT_05523 H281DRAFT_05523 propionyl-CoA synthetase (EC 6.2.1.17)

Query= SwissProt::Q9H6R3
         (686 letters)



>FitnessBrowser__Burk376:H281DRAFT_05523
          Length = 648

 Score =  613 bits (1581), Expect = e-180
 Identities = 309/625 (49%), Positives = 417/625 (66%), Gaps = 16/625 (2%)

Query: 71  TDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHIENGKGDKIA 130
           TDP  FW +AA  ++W +PW + L ++      WF     N  YN +DRH+E G+G+++A
Sbjct: 12  TDPMAFWARAASSVAWSRPWDEVLTHQPGQRFSWFDGAYTNASYNCLDRHVEAGRGEQVA 71

Query: 131 IIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQAMYTMLACAR 190
           I ++SPVT T  T TY  + +QV+  AGVL   G++ GD VVIYMP+IPQA+  MLACAR
Sbjct: 72  IAFESPVTGTAQTLTYASLRDQVAGFAGVLQLQGVRMGDVVVIYMPVIPQAIIAMLACAR 131

Query: 191 IGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEALKIGQHKPD 250
           IGA H ++FGGFA+ EL+ R+    P+V+VTAS G E  RR+ Y   V+EA+ +      
Sbjct: 132 IGATHCVVFGGFAASELAKRLRDTLPRVIVTASCGFEVKRRIPYKETVDEAV-LQSAWQG 190

Query: 251 KILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKGVI 310
            +++Y R  +  V LA  RD+DW+  M        +PV + HPLYIL+TSGTTG PKG+ 
Sbjct: 191 PVIVYQR-ELGRVELAE-RDVDWERAMCGTYGVSPIPVPAGHPLYILHTSGTTGSPKGIQ 248

Query: 311 RPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGKPV 370
           R TGGY   L WSM++IY   PG+V+WAASD+GWVVGHSY+ YGPLL+G TTVL+EGKPV
Sbjct: 249 RDTGGYMTALLWSMNNIYRSLPGDVFWAASDIGWVVGHSYMTYGPLLNGCTTVLFEGKPV 308

Query: 371 GTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGA---------ALGKQYSLTRFKTL 421
           GTPDA A++RV+A+H V  LFTAPTA+RAI+++DPG           L  +Y L   +++
Sbjct: 309 GTPDAAAFWRVIAKHRVNVLFTAPTALRAIKKEDPGGYQLREPVMGELHWRYDLGSLRSV 368

Query: 422 FVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCV--GLGNSKTPPPGQAGKSV 479
           F+AGERCD  T+EW++++  VPVLDHWWQTE G P+ AS     LG  +    G AG+++
Sbjct: 369 FLAGERCDTTTIEWAEDLLHVPVLDHWWQTEAGWPMAASTAKGALGGERRR--GAAGRAL 426

Query: 480 PGYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMD 539
           PG++V  +DD   ++ A   GN+V  LPLPPGA + +W   E ++  YF +FPG+YDT D
Sbjct: 427 PGWDVRCVDDQGAEVDAGASGNVVCGLPLPPGAMTTIWNAHERYERSYFGRFPGWYDTGD 486

Query: 540 AGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPL 599
           AGY+D +G+++VM R DDVINVAGHR+S GAIEE +     VA+CAVVG   PLKG VPL
Sbjct: 487 AGYVDADGFVFVMGRTDDVINVAGHRLSTGAIEEIVSRLDAVAECAVVGMAHPLKGQVPL 546

Query: 600 ALCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIV 659
              VL+       +      VK VR+ +G VA+ + A  V++LPKTRSGKI R +L  IV
Sbjct: 547 VFLVLKDGSKDGADAAETAAVKVVREQLGAVASMQAAFVVERLPKTRSGKILRRSLLQIV 606

Query: 660 NGKPYKITSTIEDPSIFGHVEEMLK 684
           +GK   I +TIEDP +   VE ++K
Sbjct: 607 DGKAVAIPATIEDPGVLVDVERIVK 631


Lambda     K      H
   0.318    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: 1260
Number of extensions: 61
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: 686
Length of database: 648
Length adjustment: 38
Effective length of query: 648
Effective length of database: 610
Effective search space:   395280
Effective search space used:   395280
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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