Alignments for a candidate for prpE in Azospirillum thiophilum BV-S

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Azospirillum thiophilum BV-S

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_045580972.1 AL072_RS06780 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_001305595.1:WP_045580972.1
          Length = 646

 Score =  902 bits (2330), Expect = 0.0
 Identities = 421/637 (66%), Positives = 509/637 (79%), Gaps = 3/637 (0%)

Query: 9   IPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIK 68
           +   IA    +N + Y  MY+QS+N P+ FWGE GK +DWIKPY KVK+  F  G+V I+
Sbjct: 9   VKPEIAATAHVNAEAYARMYEQSVNDPEAFWGEHGKRIDWIKPYSKVKDVDFN-GDVHIR 67

Query: 69  WYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELG 128
           W+ DGTLN++ANC+DRHL   GD+TAI++EGDD   SK I+YKELH  V R AN L + G
Sbjct: 68  WFHDGTLNVSANCIDRHLATRGDQTAILFEGDDPGVSKAITYKELHEKVSRLANVLKKNG 127

Query: 129 IKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDE 188
           ++KGD V IY+PM+PEAA AMLAC RIGA+HS++FGGFSP+++  RI+D +S  VITSDE
Sbjct: 128 VRKGDRVTIYLPMIPEAAYAMLACTRIGAIHSIVFGGFSPDSLKDRIVDCDSHFVITSDE 187

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

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

Query: 309 WVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEG 368
           WVTGHSY++YGPLA GATTLMFEGVP +P  +R  QV+DKH+VNI YTAPTAIR+LM EG
Sbjct: 306 WVTGHSYIVYGPLANGATTLMFEGVPTYPDVSRFWQVIDKHKVNIFYTAPTAIRSLMREG 365

Query: 369 DKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPG 428
           +  ++ T R+SLR+LGSVGEPINPEAW WY+  +G+ +CP+VDTWWQTETGG +ITPL G
Sbjct: 366 EGPVKTTSRASLRVLGSVGEPINPEAWLWYYNVVGDARCPIVDTWWQTETGGILITPLIG 425

Query: 429 ATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTY 488
           A   K GSAT+PFFGVQP +VDNEG  LEG TEG+L I D+WPG  RT++GDHERF QTY
Sbjct: 426 AIGQKPGSATKPFFGVQPVVVDNEGQVLEGETEGNLCIADAWPGMMRTVYGDHERFVQTY 485

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

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

Query: 609 KIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           KIMRRILRKIAA +   LGDTSTLADPGVV  L++ +
Sbjct: 606 KIMRRILRKIAANEHDALGDTSTLADPGVVTDLIDNR 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: 1490
Number of extensions: 68
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 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources