GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Pseudomonas fluorescens FW300-N2E2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Pf6N2E2_5659 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659
          Length = 646

 Score =  950 bits (2455), Expect = 0.0
 Identities = 446/637 (70%), Positives = 524/637 (82%)

Query: 7   HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66
           + +   +A   L +   Y+AMYQQS+  PD FW EQ K LDWIKP+  VK TSF   +V 
Sbjct: 2   YPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 61

Query: 67  IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126
           IKW+ DGTLN++ NCLDRHL E GD+ AIIWEGDD ++S++I+Y+ELH +VC+FAN L  
Sbjct: 62  IKWFADGTLNVSYNCLDRHLAERGDQVAIIWEGDDPAESRNITYRELHEEVCKFANALRG 121

Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186
             + +GDVV IYMPM+PEA VAMLACARIGA+HSV+FGGFSPEA+AGRIID  S++VIT+
Sbjct: 122 QDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 181

Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASD 246
           DEGVRAG+ IPLK NVDDAL NP  +S++ V+V KRT G I W + RD+W+ DL++ A  
Sbjct: 182 DEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAGT 241

Query: 247 QHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTAD 306
               +EM AE+ LFILYTSGSTGKPKGV HTT GYL+YAALT + VFDY PGD+YWCTAD
Sbjct: 242 VCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGDVYWCTAD 301

Query: 307 VGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMA 366
           VGWVTGHSY++YGPLA GATTL+FEGVPN+P   R+A+VVDKH+VNILYTAPTAIRA+MA
Sbjct: 302 VGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVVDKHKVNILYTAPTAIRAMMA 361

Query: 367 EGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPL 426
            G  A+EG D SSLR+LGSVGEPINPEAW+WY+K +G E+CP+VDTWWQTETGG +I+PL
Sbjct: 362 SGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISPL 421

Query: 427 PGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQ 486
           PGAT LK GSATRPFFGV PALVDN GN +EGA EG+LVI DSWPGQARTL+GDH+RF  
Sbjct: 422 PGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFVD 481

Query: 487 TYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAA 546
           TYF TF  MYF+GDGARRDEDGYYWITGRVDDVLNVSGHR+GTAEIESA+VAHPK+AEAA
Sbjct: 482 TYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAA 541

Query: 547 VVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTR 606
           VVG+PH+IKGQ IY YVTLN GEE S  L  E++NWVRKEIGP+A+PDV+ W   LPKTR
Sbjct: 542 VVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTR 601

Query: 607 SGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLE 643
           SGKIMRRILRKIA  +   LGD STLADP VV  L+E
Sbjct: 602 SGKIMRRILRKIATAEYDGLGDISTLADPSVVAHLIE 638


Lambda     K      H
   0.317    0.135    0.421 

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: 1515
Number of extensions: 60
Number of successful extensions: 1
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: 652
Length of database: 646
Length adjustment: 38
Effective length of query: 614
Effective length of database: 608
Effective search space:   373312
Effective search space used:   373312
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