Alignments for a candidate for prpE in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Pedobacter sp. GW460-11-11-14-LB5

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate CA265_RS16340 CA265_RS16340 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Pedo557:CA265_RS16340
          Length = 631

 Score =  733 bits (1891), Expect = 0.0
 Identities = 360/625 (57%), Positives = 455/625 (72%), Gaps = 10/625 (1%)

Query: 22  QQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANC 81
           +QYE  Y++S+  P+ FWGE  +   W KP+ KV + +F   N  IKW+E   LN+  NC
Sbjct: 7   KQYEEDYKKSVENPEQFWGEVAQNFQWRKPWFKVLSWNFNEPN--IKWFEGAKLNITENC 64

Query: 82  LDRHLQENGDRTAIIWEGDDASQ-SKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMP 140
           LDRHL  NGD+ AI+WE ++  + S   +YK LH  VCRFAN L   G KKGD + IYMP
Sbjct: 65  LDRHLATNGDKPAIVWEPNNPEEESVTYTYKMLHERVCRFANVLKRNGAKKGDRICIYMP 124

Query: 141 MVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKK 200
           MVPE A+A+LACARIGAVHSVIFGGFS +++A RI DS  ++VIT+D   R  + IPLK 
Sbjct: 125 MVPELAIAVLACARIGAVHSVIFGGFSAKSIADRINDSKCKVVITADGSYRGNKQIPLKD 184

Query: 201 NVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPLF 260
            +DDAL      +VE  +VL      +   +GRD+WW D V+  +D  +AEEM+AED LF
Sbjct: 185 VIDDALIG--CPTVEKCIVLTHIRTPVSMLKGRDVWWEDEVKHVNDICEAEEMDAEDMLF 242

Query: 261 ILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGP 320
           ILYTSGSTGKPKGV+HT GGY+VYA  TF  VF+Y PG++Y+CTAD+GW+TGHSY++YGP
Sbjct: 243 ILYTSGSTGKPKGVVHTCGGYMVYAGYTFSNVFNYQPGEVYFCTADIGWITGHSYIVYGP 302

Query: 321 LACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSL 380
           L+ GAT+++FEG+P +PTP+R   +V+KH+VN LYTAPTAIR+LM+ GD  + G D SS+
Sbjct: 303 LSQGATSVLFEGIPTYPTPSRFWDIVEKHKVNTLYTAPTAIRSLMSYGDDPLNGKDLSSI 362

Query: 381 RILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRP 440
           R+LGSVGEPIN EAW W+ +KIG+ K P+VDTWWQTETGG MI+P+   T  K   AT P
Sbjct: 363 RVLGSVGEPINEEAWHWFDEKIGHGKAPIVDTWWQTETGGIMISPIATVTPTKPSFATLP 422

Query: 441 FFGVQPALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSG 499
             G+QP LVD  GN +EG    G+L I   WPG  RT +GDHER +QTYFST+ N+YF+G
Sbjct: 423 LPGIQPILVDENGNEIEGNGVMGNLCIKFPWPGMLRTTYGDHERCKQTYFSTYDNLYFTG 482

Query: 500 DGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAI 559
           DG  RDEDGYY ITGRVDDVLNVSGHR+GTAE+E+A+  H  + E+AVVG PH++KGQ I
Sbjct: 483 DGCLRDEDGYYRITGRVDDVLNVSGHRIGTAEVENAINMHAGVVESAVVGYPHDVKGQGI 542

Query: 560 YAYVTL--NHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617
           YA+V     HGE    +   ++   V + IG +A PD + +   LPKTRSGKIMRRILRK
Sbjct: 543 YAFVIYPEMHGEAELSK--KDILQTVTRVIGAIAKPDKILFVSGLPKTRSGKIMRRILRK 600

Query: 618 IAAGDTSNLGDTSTLADPGVVEKLL 642
           IA GDTSNLGDTSTL DPGVVE+++
Sbjct: 601 IAEGDTSNLGDTSTLLDPGVVEEII 625


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: 1327
Number of extensions: 59
Number of successful extensions: 6
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: 631
Length adjustment: 38
Effective length of query: 614
Effective length of database: 593
Effective search space:   364102
Effective search space used:   364102
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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Protein sequences (fasta format)
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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:

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