GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Pseudomonas fluorescens FW300-N2E3

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate AO353_14365 AO353_14365 acetyl-CoA synthetase

Query= SwissProt::P27550
         (652 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 AO353_14365 acetyl-CoA
           synthetase
          Length = 645

 Score =  814 bits (2103), Expect = 0.0
 Identities = 383/628 (60%), Positives = 484/628 (77%), Gaps = 5/628 (0%)

Query: 19  INPQQYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNL 77
           ++   Y+ +Y+QSI  PD FW EQ K  LDW  P+Q V++T+   G  + +W+    LN+
Sbjct: 19  LSQDDYQRLYRQSIEQPDVFWAEQAKRFLDWSTPWQSVQHTNIKTG--AAQWFAGAQLNV 76

Query: 78  AANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAI 137
           + NC+DRHL + G++TAIIWEGDD ++S HI+Y++LH  VCR AN L   G+KKGD V I
Sbjct: 77  SYNCIDRHLAQRGEQTAIIWEGDDPAESLHITYQKLHHCVCRLANVLKSRGVKKGDRVCI 136

Query: 138 YMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIP 197
           YMPM+PEAA AMLACARIGAVHSV+FGGFSP+++  RI+D++ R VIT+DEGVR G+ +P
Sbjct: 137 YMPMIPEAAYAMLACARIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGKYVP 196

Query: 198 LKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAED 257
           LK+NVD AL +    +V  VVV++ T  +++W EGRDLW+H  +   SD    E M+AED
Sbjct: 197 LKQNVDKALLS--CPAVSTVVVVEHTQIEVNWVEGRDLWYHQALRDVSDDCPPEPMDAED 254

Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317
           PLFILYTSGSTGKPKGVLHTTGGYL+ AA+TFKYVFDY  G+++WCTADVGWVTGHSY++
Sbjct: 255 PLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGEVFWCTADVGWVTGHSYIV 314

Query: 318 YGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377
           YGPLA GATTL+FEGVP++P  +R  QV+DKHQVNI YTAPTA+RALM EG + ++ + R
Sbjct: 315 YGPLANGATTLIFEGVPSYPNSSRFWQVIDKHQVNIFYTAPTALRALMREGLEPLKDSSR 374

Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSA 437
           +SLR+LGSVGEPINPEAW+WY+  +G ++CP+VDTWWQTETGG M++PL  A  +K G A
Sbjct: 375 ASLRLLGSVGEPINPEAWDWYFNAVGEQRCPIVDTWWQTETGGIMLSPLVSAQRIKPGCA 434

Query: 438 TRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYF 497
           TRP FGVQP L+D  G  + GA  G L I  SWPGQ R+++GD +R   TYF  +   YF
Sbjct: 435 TRPMFGVQPVLLDEHGKEISGAGSGVLAIKSSWPGQIRSVYGDPQRMIDTYFKPYPGYYF 494

Query: 498 SGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQ 557
           +GDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESALV H  IAEAAVVG PH++KGQ
Sbjct: 495 TGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIAEAAVVGYPHDLKGQ 554

Query: 558 AIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617
            IYA+VT  +G EPS  L  E+   V +EIG  A PD++ W  +LPKTRSGKIMRRILRK
Sbjct: 555 GIYAFVTPMNGIEPSDALKKELLAHVSQEIGSFAKPDLIQWAPALPKTRSGKIMRRILRK 614

Query: 618 IAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           IA  +  +LGDTSTLADP VV  L++++
Sbjct: 615 IACNELDSLGDTSTLADPSVVAGLIDKR 642


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: 1373
Number of extensions: 54
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: 652
Length of database: 645
Length adjustment: 38
Effective length of query: 614
Effective length of database: 607
Effective search space:   372698
Effective search space used:   372698
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 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