GapMind for catabolism of small carbon sources

 

Alignments 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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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