GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_2351
          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:

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