GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Azospirillum brasilense Sp245

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate AZOBR_RS00270 AZOBR_RS00270 acetyl-CoA synthetase

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__azobra:AZOBR_RS00270
          Length = 646

 Score =  919 bits (2374), Expect = 0.0
 Identities = 430/637 (67%), Positives = 515/637 (80%), Gaps = 3/637 (0%)

Query: 9   IPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIK 68
           +   IA    ++   Y  +Y+QSIN P+ FWGEQGK +DWIKPY KVK+ S+  G+V IK
Sbjct: 9   VKQEIAKTAYVDEAAYARLYEQSINDPEAFWGEQGKRIDWIKPYSKVKDVSYT-GDVHIK 67

Query: 69  WYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELG 128
           W+ DGTLN++ANC+DRHL   GD+TAII+EGDD   SKHI+YKELH  VCR AN L + G
Sbjct: 68  WFYDGTLNVSANCVDRHLATRGDQTAIIFEGDDPGVSKHITYKELHEQVCRLANVLKKNG 127

Query: 129 IKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDE 188
           +KKGD V IY+PM+PEAA AMLACAR+GA+HS++FGGFSP+++  RI+D +S  VITSDE
Sbjct: 128 VKKGDRVTIYLPMIPEAAYAMLACARVGAIHSIVFGGFSPDSLKDRIVDCDSHFVITSDE 187

Query: 189 GVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQH 248
           G+R GR +PLK N D A+       V+HV+V+K TGG + W EGRDLW+H+ +   S   
Sbjct: 188 GLRGGRKVPLKANADKAVAA--APGVKHVLVVKHTGGNVAWTEGRDLWYHEEIASVSADC 245

Query: 249 QAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVG 308
             EEM+AEDPLFILYTSGSTGKPKGVLHTTGGYLVYA++T +YVFDY  G++YWCTADVG
Sbjct: 246 PPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYKDGEVYWCTADVG 305

Query: 309 WVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEG 368
           WVTGHSY++YGPLA GATTLMFEGVP +P  +R  QVVDKH+VNI YTAPTAIR+LM EG
Sbjct: 306 WVTGHSYIVYGPLANGATTLMFEGVPTYPDISRFWQVVDKHKVNIFYTAPTAIRSLMREG 365

Query: 369 DKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPG 428
           +  ++ T RSSLRILGSVGEPINPEAW WY+  +G+ +CP+VDTWWQTETGG +ITPLPG
Sbjct: 366 EGPVKKTSRSSLRILGSVGEPINPEAWLWYYNVVGDGRCPIVDTWWQTETGGILITPLPG 425

Query: 429 ATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTY 488
           A   K GSAT+PFFGV+P +VDN+G  LEG TEG+L I DSWPGQ RT+FGDHERF QTY
Sbjct: 426 AIGQKPGSATKPFFGVKPVVVDNDGKELEGETEGNLCIADSWPGQMRTVFGDHERFVQTY 485

Query: 489 FSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVV 548
           FSTF   YF+GDG RRD DGYYWITGRVDDV+NVSGHR+GTAE+ESALVAHPK+AEAAVV
Sbjct: 486 FSTFAGYYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHPKVAEAAVV 545

Query: 549 GIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSG 608
           G PH++KGQ IYAYVTLN GE P+ EL  E+  WVRKEIGP+A+PD++ W+  LPKTRSG
Sbjct: 546 GYPHDLKGQGIYAYVTLNAGESPTEELRKELVAWVRKEIGPIASPDLIQWSPGLPKTRSG 605

Query: 609 KIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           KIMRRILRKIAA +  +LGDTSTLADP VV  L+E +
Sbjct: 606 KIMRRILRKIAANEHDSLGDTSTLADPTVVTDLIENR 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: 1487
Number of extensions: 62
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: 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