GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhodobacter maris JA276

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_097069234.1 CRO22_RS06000 propionyl-CoA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_900217815.1:WP_097069234.1
          Length = 631

 Score =  655 bits (1690), Expect = 0.0
 Identities = 318/623 (51%), Positives = 422/623 (67%), Gaps = 3/623 (0%)

Query: 58  YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHI 117
           Y   + A  ADPE FW +AA+ I W +P +K    +  P+  WF +  +N C+NAIDRH+
Sbjct: 3   YNEVYGAWKADPEGFWMEAAKGIDWVEPPSKAFFEQ-GPAGEWFADAKVNTCWNAIDRHV 61

Query: 118 ENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQA 177
           E G+GD+IAI+++SP+T     I+YKE+  +VS LAG L  +GV+KGD V+IYMPMIP+A
Sbjct: 62  EAGRGDQIAIMHESPITHATKGITYKELKARVSSLAGALRMRGVEKGDRVIIYMPMIPEA 121

Query: 178 IYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEA 237
           + AMLACARIGAIHS++FGGFA+ EL+ RID   PK ++ AS G+EP R V Y PLL+ A
Sbjct: 122 LEAMLACARIGAIHSVVFGGFAAHELAVRIDDCTPKAIIAASCGLEPNRVVHYKPLLDAA 181

Query: 238 LRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSG 297
           +    HKP+  +I+ R   E   L+ GRD  W       +  +CVPV   HP YILYTSG
Sbjct: 182 IDQATHKPEFCVIFQR-EQEVAKLVEGRDFSWHGFQYGVKPAECVPVDGNHPAYILYTSG 240

Query: 298 TTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNT 357
           TTG PKGVVR T G+ V LNW+M +IY ++ G+ +WAASD+GWVVGHSYICY PLL G T
Sbjct: 241 TTGAPKGVVRATAGHLVALNWSMKAIYNIEAGDRFWAASDVGWVVGHSYICYAPLLAGAT 300

Query: 358 TVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTL 417
           TV++EGKPVGTP  G ++R++  H + + FTAPTA+RAIR++DP     K+Y L   + L
Sbjct: 301 TVVFEGKPVGTPHPGVFWRIIQNHRIKSFFTAPTALRAIRREDPNGEYIKRYKLHEMQAL 360

Query: 418 FVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPG 477
           F+AGER D +T+ W+++   VPV+DHWWQTETG  I  + +G+        G   K +PG
Sbjct: 361 FLAGERADPDTVNWAREHLGVPVIDHWWQTETGWAIAGNPLGI-ELLPVKVGSPTKAMPG 419

Query: 478 YNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAG 537
           Y+V +LD+    +   +LG I +KLPLPPG    LW  +E F   Y   FPGYY+T DAG
Sbjct: 420 YDVQVLDEGGHPVPPGTLGAIAIKLPLPPGTLPTLWNAEERFVKSYLNHFPGYYETGDAG 479

Query: 538 YMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLAL 597
           Y+DE+GY+Y+M+R DDVINVAGHR+S GA+EE + SH  V +CAV+G  D LKG +P+  
Sbjct: 480 YIDEDGYVYIMARTDDVINVAGHRLSTGAMEEVLASHPDVAECAVIGVSDELKGQLPMGF 539

Query: 598 CVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNG 657
             L K       QV++E V  VR  IGPVAAF+ AV V +LPKTRSGKI R T+  + +G
Sbjct: 540 LCLNKGCTKAHAQVIKECVNLVRDQIGPVAAFKLAVVVDRLPKTRSGKILRGTMVKIADG 599

Query: 658 KPYKVTPTIEDPSIFGHIEEVLK 680
           +P+K+  TI+DP+I   I   LK
Sbjct: 600 EPFKMPATIDDPTILDEIAAALK 622


Lambda     K      H
   0.318    0.136    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: 1390
Number of extensions: 62
Number of successful extensions: 4
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: 683
Length of database: 631
Length adjustment: 38
Effective length of query: 645
Effective length of database: 593
Effective search space:   382485
Effective search space used:   382485
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