GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Pseudomonas putida KT2440

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 PP_2351 PP_2351 propionyl-CoA synthetase

Query= SwissProt::Q9H6R3
         (686 letters)



>lcl|FitnessBrowser__Putida:PP_2351 PP_2351 propionyl-CoA synthetase
          Length = 629

 Score =  656 bits (1692), Expect = 0.0
 Identities = 313/622 (50%), Positives = 431/622 (69%), Gaps = 2/622 (0%)

Query: 62  YKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHI 121
           Y+  +A S++DP  FW + A  ++W++    TL++    + RWF +G LN CY A+D  I
Sbjct: 3   YQHSYAHSISDPAAFWAEQAAHLAWHRKPALTLQDNADGTHRWFADGRLNSCYLALDHQI 62

Query: 122 ENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQA 181
           E G+G+++A+IYDSPVT  + T+TY ++ ++V++LAG+L + G+ KGD V+IYMPM+PQA
Sbjct: 63  EQGRGEQLALIYDSPVTGVQQTYTYNQLRDEVARLAGLLRQLGVNKGDGVIIYMPMVPQA 122

Query: 182 MYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEA 241
              MLACARIGA+HS++FGGFA+ EL+ RID  +P +++TAS G+E  R + Y PLV+ A
Sbjct: 123 AMAMLACARIGAVHSVVFGGFAANELALRIDDARPTLLLTASCGLEFDRVIAYKPLVDRA 182

Query: 242 LKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTSG 301
           L++ +H+P  +L+  RP   A  L PGRDLDW   +A A+    V + +  PLYI+YTSG
Sbjct: 183 LQLARHQPRNVLVLQRPQAHA-ELLPGRDLDWQAALADAEPVAPVELDAGDPLYIMYTSG 241

Query: 302 TTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNT 361
           TTG PKG++R  GG AV L ++M  IYG+Q G+VWW  SD+GWVVGHS I YGPL+ G T
Sbjct: 242 TTGKPKGIVRENGGNAVALCYAMRHIYGMQAGDVWWGISDVGWVVGHSLIVYGPLMSGCT 301

Query: 362 TVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTL 421
           TV YEGKP+ TPDA AY+RV+ ++ V ALF APTA+RAIR++DP   L +++ L+  + L
Sbjct: 302 TVFYEGKPIRTPDASAYWRVVEQYRVNALFCAPTAMRAIRKEDPEGDLIRKHDLSSLRQL 361

Query: 422 FVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKSVPG 481
           F+AGE+ D  T EW + V   PV DHWWQTETG P+TA CVGL  S    PG + ++VPG
Sbjct: 362 FLAGEKLDSSTHEWLERVSGKPVHDHWWQTETGWPVTAPCVGLEGS-AAKPGSSNRAVPG 420

Query: 482 YNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAG 541
           YNV +LDD    L A   G+IV+ LPLPPG    LW + E +   Y   +PGYY T D G
Sbjct: 421 YNVRVLDDEGHLLGANHQGSIVIALPLPPGCSQTLWGDHERYLQAYLRTYPGYYHTGDGG 480

Query: 542 YMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPLAL 601
           Y+D++G++Y+M R DDVINV+GHR+S G +E+ +  H  VA+CAV+G  D +KG VPLAL
Sbjct: 481 YLDDDGFVYIMGRTDDVINVSGHRLSTGEMEDLVARHPAVAECAVIGVHDEIKGQVPLAL 540

Query: 602 CVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIVNG 661
            VL+      E Q+L E+V  VR+ IGP+A F     VK+LPKTRSGKI R+ L  I +G
Sbjct: 541 VVLKDGEGIAEAQLLVELVGSVREEIGPLACFNRVRLVKRLPKTRSGKILRAVLRKIADG 600

Query: 662 KPYKITSTIEDPSIFGHVEEML 683
           + Y   ST++DP++ G +E +L
Sbjct: 601 QDYVPPSTLDDPAVLGEIEAVL 622


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: 1118
Number of extensions: 46
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: 686
Length of database: 629
Length adjustment: 38
Effective length of query: 648
Effective length of database: 591
Effective search space:   382968
Effective search space used:   382968
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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