GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Brucella microti CCM 4915

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_015799731.1 BMI_RS08045 propionyl-CoA synthetase

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



>NCBI__GCF_000022745.1:WP_015799731.1
          Length = 636

 Score =  806 bits (2082), Expect = 0.0
 Identities = 389/637 (61%), Positives = 480/637 (75%), Gaps = 14/637 (2%)

Query: 2   SYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLY-EWFADARVNTCYNAVDR 60
           +Y+E Y  W+ +PE FW +AA AI W   P + +   G+G Y  W+  A  NTCYNA+DR
Sbjct: 4   NYAETYAAWQNDPEGFWADAAAAIDWFK-PWEQVFAGGEGTYGRWYTGAECNTCYNALDR 62

Query: 61  HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120
           HV  GRG+Q A+IY+SPIT   R+I+Y EL   V  LA  +   GV+KGDR++IYMP +P
Sbjct: 63  HVANGRGDQLALIYESPITGKTRKITYHELLEEVEALAAVMLDNGVQKGDRILIYMPTVP 122

Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180
           EA+ AMLA AR+GA+HSVVFGGFAANELA RIDDA P  IIAASCG+EP R V Y+ +LD
Sbjct: 123 EAVVAMLASARIGAIHSVVFGGFAANELATRIDDAKPVMIIAASCGIEPSRVVPYQAMLD 182

Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAE-----CVPVEGNHPAY 235
            AI LA HK D C+IFQREQ     +EGRD++   ++  V+ A      CVPV    P Y
Sbjct: 183 KAISLAHHKVDHCIIFQREQHRHLPVEGRDID---YREAVDAARGRHVPCVPVAATDPLY 239

Query: 236 ILYTSGTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGP 295
           +LYTSGTTG+PKGV+R   G +VAL W+MK++++V PG V+WAASDVGWVVGHSYI Y P
Sbjct: 240 VLYTSGTTGEPKGVVRDNGGHMVALVWSMKHVFDVKPGQVWWAASDVGWVVGHSYIVYAP 299

Query: 296 LIHGNTTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDL 355
           L+ G T+I+FEGKP+GTPDAG +WR+I EH V+  FTAPTA RA+K+ED  G FV+++DL
Sbjct: 300 LLIGATSILFEGKPVGTPDAGEYWRIIEEHGVEVMFTAPTALRAIKKEDADGHFVRRHDL 359

Query: 356 SCLKQVYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPA 415
           S  + +YLAGERADP+TI WA+  L  PVIDHWWQTE+GW + ANPLG+  L TK GSPA
Sbjct: 360 SGFRALYLAGERADPETIHWAENLLGCPVIDHWWQTESGWPMVANPLGLGLLETKYGSPA 419

Query: 416 VPMPGYTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYE 475
           V +PGY + +LD+ GH V PG LG I +KLPLPPG LPTLWNA++RF+K+YL  FPGYY+
Sbjct: 420 VCLPGYDIRVLDDEGHEVEPGTLGNILIKLPLPPGCLPTLWNADERFRKAYLNEFPGYYK 479

Query: 476 TGDAGMKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQ 535
           T DAG  DEDGYLYIM+RTDD+INVAGHRLSTGAMEEVL+ HPDVAECAV+G+SD LKGQ
Sbjct: 480 TADAGYMDEDGYLYIMSRTDDIINVAGHRLSTGAMEEVLSSHPDVAECAVLGISDPLKGQ 539

Query: 536 APVGFLCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMV 595
            P GFL L +  D   ++V  + + ++R+ IGPVAAF+LA  V RLPKTRSGKILR T+ 
Sbjct: 540 VPCGFLVLKSNIDRDPQEVEKECISMIRDAIGPVAAFRLALAVKRLPKTRSGKILRSTIQ 599

Query: 596 NIADGTDWKMPATIDDPAILDEITTALQ----GLGYA 628
            +ADG +WKMPATIDDPAILDEI T L+    GL +A
Sbjct: 600 KMADGQEWKMPATIDDPAILDEIGTVLRERHIGLAFA 636


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: 1406
Number of extensions: 53
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: 629
Length of database: 636
Length adjustment: 38
Effective length of query: 591
Effective length of database: 598
Effective search space:   353418
Effective search space used:   353418
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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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