Alignments for a candidate for prpE in Chryseobacterium arthrosphaerae CC-VM-7

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Chryseobacterium arthrosphaerae CC-VM-7

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_065397344.1 BBI00_RS02810 AMP-binding protein

Query= reanno::Phaeo:GFF1175
         (629 letters)



>NCBI__GCF_001684965.1:WP_065397344.1
          Length = 628

 Score =  657 bits (1694), Expect = 0.0
 Identities = 311/606 (51%), Positives = 417/606 (68%), Gaps = 3/606 (0%)

Query: 15  EQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHVEQGRGEQTAIIY 74
           E FW + AEAI W   P + L+   +   +W++D R+N C+  +D+H+E G G+QTAI+Y
Sbjct: 15  EDFWKQQAEAIQWFEFPQQILSKDQNNYPQWYSDGRLNMCHLCIDQHIEDGFGDQTAIVY 74

Query: 75  DSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEALEAMLACARLGA 134
           DSP+T  K+  ++ + +  ++ LAG L + G++KGD  +IYMPMIP+ L AMLACAR+G 
Sbjct: 75  DSPVTGQKKTYTFRQAQEEISKLAGGLASLGLKKGDTAVIYMPMIPQTLFAMLACARIGV 134

Query: 135 VHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGAIDLATHKPDFCV 194
           +H+VVFGGFA +EL VRIDD  PK +I A+ G+E  + + Y PL++ AI+LA  K D  +
Sbjct: 135 IHNVVFGGFAPHELVVRIDDCKPKVLITATAGIEIAKRIPYLPLVEKAIELAQDKVDNII 194

Query: 195 IFQRE--QEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSGTTGQPKGVIRH 252
           ++ R+      E+ +G  +++       EPA+CV VE  HP Y+LYTSGTTG+PKG++R 
Sbjct: 195 VYNRKLVDNQHEMFDGL-IDYEELVQKSEPADCVSVESTHPLYLLYTSGTTGKPKGIVRD 253

Query: 253 TAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTTIVFEGKPIGT 312
           T G   AL ++MK IY V+PG+ +WAASD GW VGHS+  YGPLI+ NTTI+FEGKPI T
Sbjct: 254 TGGYATALKFSMKYIYGVEPGETYWAASDFGWAVGHSFSVYGPLINRNTTIIFEGKPIMT 313

Query: 313 PDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQVYLAGERADPDT 372
           PDAGTFWR+ISE+KV   FTAPTA RA+K+EDP GE VKKYDLS  K+ +LAGER D  T
Sbjct: 314 PDAGTFWRIISEYKVSVMFTAPTAIRAIKKEDPDGELVKKYDLSHFKKQFLAGERCDVAT 373

Query: 373 ITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGYTVDILDEGGHP 432
           + W  E + VP IDHWWQTE+GW +       E    K  S   P+PGY + I DE G+ 
Sbjct: 374 LDWFAEHIGVPAIDHWWQTESGWPMLGLMTFDENYKIKRASAGKPVPGYDIKIFDENGYE 433

Query: 433 VAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGMKDEDGYLYIMA 492
           +   + G + +KLPLPPG +  +WN  +RF  SYL+ + GYY +GD  ++DEDGY++I  
Sbjct: 434 LDAHQEGYLIIKLPLPPGAMLGIWNDYERFHNSYLSQYNGYYFSGDGAIQDEDGYIFITG 493

Query: 493 RTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFLCLNAGCDTPHE 552
           R DDVINVAGHRLST  MEE+++ HPDVAECAV+G+ D LKGQ P   + L  G     E
Sbjct: 494 RVDDVINVAGHRLSTSEMEEIVSSHPDVAECAVVGIDDDLKGQIPFASVVLKNGAAISEE 553

Query: 553 DVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGTDWKMPATIDDP 612
            V   ++++VREKIG VA  K A VV RLPKTRSGK LR  +  + DG D+++P+TIDD 
Sbjct: 554 QVEKDIIRMVREKIGAVAFLKNAMVVKRLPKTRSGKTLRKLIRTLLDGKDFQVPSTIDDE 613

Query: 613 AILDEI 618
            I++EI
Sbjct: 614 KIIEEI 619


Lambda     K      H
   0.318    0.137    0.428 

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: 1177
Number of extensions: 49
Number of successful extensions: 2
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: 629
Length of database: 628
Length adjustment: 38
Effective length of query: 591
Effective length of database: 590
Effective search space:   348690
Effective search space used:   348690
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.

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