Alignments for a candidate for prpE in Saccharomonospora marina XMU15

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Saccharomonospora marina XMU15

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_009156574.1 SACMADRAFT_RS24615 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000244955.1:WP_009156574.1
          Length = 659

 Score =  669 bits (1726), Expect = 0.0
 Identities = 347/658 (52%), Positives = 451/658 (68%), Gaps = 24/658 (3%)

Query: 3   AIESVMQEHRVFNPPEGFASQA-AIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61
           A+++++ E R F P E FA++A A P   A      EAE+D E FWAR A E LHW   +
Sbjct: 7   ALDNLLTESRTFPPSEEFAARANATPEWYA------EAEQDREAFWARQA-ERLHWDTRW 59

Query: 62  TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121
           ++VLD S APF KWF  G+LN +YNC+DR+++ G+ D+VAI +  + G    +TY +L  
Sbjct: 60  SQVLDWSQAPFAKWFVGGKLNVAYNCVDRHVEAGHGDQVAIHWVGEPGDTRDITYAQLKD 119

Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181
           +VC+ AN L +LG+   DRV I + M  E +VAM ACAR+GA HSVVFGGFS  +L+ R+
Sbjct: 120 EVCKAANALTSLGVTANDRVAIQLQMIPEAIVAMLACARIGAMHSVVFGGFSPTALRSRV 179

Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDR 241
            D  A  +IT+D Q R GKA P+KA  D+ALA  G E+V  V+V RRTG  V WT+ RD 
Sbjct: 180 DDAQAKVVITSDGQYRRGKAAPMKANVDEALA--GAESVEKVVVVRRTGDDVPWTQERDL 237

Query: 242 WMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDI 301
           W  ++   QP     +   +EHPL++LYTSG+TGKPKG+ H++GGYL     T    FD 
Sbjct: 238 WWHELVDPQPAEHTPQAFDSEHPLYILYTSGTTGKPKGILHTSGGYLAHVAYTHHAVFDH 297

Query: 302 KP-DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
           KP +D++WCTADIGWVTGH+YI YGPLA   TQVV+EG P  P+ GR W++I ++KVSI+
Sbjct: 298 KPGEDVYWCTADIGWVTGHSYIVYGPLANRVTQVVYEGTPNTPHEGRHWEIIQKYKVSIY 357

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPT IR+ +K         P +YDLSSLR+LG+VGEPINPEAWMWY ++IG  RCP+V
Sbjct: 358 YTAPTLIRTFMKWGNEI----PAKYDLSSLRVLGSVGEPINPEAWMWYREHIGGNRCPVV 413

Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480
           DT+WQTETGG MI+PLPG T   PGS   PLPGI A +VD+TG +V  G GG LV+ +PW
Sbjct: 414 DTWWQTETGGIMISPLPGVTHAKPGSAQRPLPGISAKVVDDTGTEVGKGGGGYLVLDKPW 473

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           P M+R IWGD ER++++Y+        Y AGDG+  D D G   ++GR+DDV+NVSGHR+
Sbjct: 474 PGMLRGIWGDDERYKETYWSRFAEQGFYFAGDGAKYDAD-GDIWLLGRVDDVMNVSGHRI 532

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLK----RSRPTGEEAVKIATELR 596
            T E+ESALVS+P VAEAAVVG  D  TG+ I AFV+L+         G EA++    LR
Sbjct: 533 STTEVESALVSHPTVAEAAVVGATDPTTGQGIVAFVILRGGVAEDEAGGTEAIQ---ALR 589

Query: 597 NWVGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILE 654
           N V KEIGPIAKP+ I     LPKTRSGKIMRRLLR +A+  EI  D +TL + ++++
Sbjct: 590 NHVAKEIGPIAKPRQIMVVPELPKTRSGKIMRRLLRDVAENREI-GDVTTLADSSVMD 646


Lambda     K      H
   0.319    0.136    0.422 

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: 1436
Number of extensions: 67
Number of successful extensions: 9
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: 660
Length of database: 659
Length adjustment: 38
Effective length of query: 622
Effective length of database: 621
Effective search space:   386262
Effective search space used:   386262
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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.

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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