GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Halioglobus japonicus S1-36

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_084199287.1 C0029_RS09450 propionyl-CoA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_002869505.1:WP_084199287.1
          Length = 618

 Score =  692 bits (1785), Expect = 0.0
 Identities = 320/608 (52%), Positives = 440/608 (72%), Gaps = 2/608 (0%)

Query: 73  WGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQGDKIAIIYDSP 132
           W +AA+ + W+K   + L++  PP   WF +G  N CYNA+D H+  G+G++ A+IYDSP
Sbjct: 7   WREAAQAVHWFKTPQQVLDDSEPPFYRWFPDGQTNACYNALDVHVAEGRGEQTALIYDSP 66

Query: 133 VTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAMLACARIGAIHS 192
           VTDT    +Y ++L+QV++ AGVL   GV +GD V++YMPM+P+A+ AMLACAR+GA+HS
Sbjct: 67  VTDTCRRYTYTQLLDQVARFAGVLADHGVGRGDRVIVYMPMVPEALIAMLACARLGAVHS 126

Query: 193 LIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQHKPDRLLIYN 252
           ++FGGFAS EL+ RID   PK++V+AS G+EP R V Y PLL+ A+ + QHKPD  +I  
Sbjct: 127 VVFGGFASNELAVRIDDATPKLIVSASCGVEPNRIVAYKPLLDAAIELAQHKPDNCVILQ 186

Query: 253 RPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKGVVRPTGGY 312
           RP M+   L++GRD+DW + MA A++  C PV +  PLY+LYTSGTTG PKGVVR TGG 
Sbjct: 187 RP-MQPAELIAGRDVDWTQAMADARAVPCTPVAANDPLYVLYTSGTTGQPKGVVRDTGGS 245

Query: 313 AVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGKPVGTPDAG 372
            V L W+M +IY ++PG+V+WAASD+GWVVGHSYI YGPL  G  TV+YEGKPVGTPD G
Sbjct: 246 IVALKWSMKAIYDVEPGDVYWAASDVGWVVGHSYIVYGPLFSGCATVIYEGKPVGTPDPG 305

Query: 373 AYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGERCDVETLEWS 432
           A++RV+ ++ V  LFTAPTA RAI+++DP     +QY+++  ++LF+AGERCD  TL W+
Sbjct: 306 AFWRVIEDYQVKVLFTAPTAFRAIKKEDPAGKYLQQYNVSSLRSLFLAGERCDPSTLAWA 365

Query: 433 KKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPGYNVMILDDNMQKLKA 492
           ++  +VPV+DHWWQTETG PI A+C+G+  +    PG   + VPGY V +LD N +++ A
Sbjct: 366 QQQLKVPVIDHWWQTETGWPICANCLGI-EALPIVPGSPARPVPGYYVQVLDGNGEQVSA 424

Query: 493 RSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEEGYLYVMSRVD 552
             +G +VVK PLPPG F+ LW+ +E ++  YF ++PGYY+T DAGY+D  GY++VM+R D
Sbjct: 425 GEIGALVVKSPLPPGTFTTLWQAEERYQSAYFARYPGYYETGDAGYIDANGYVFVMARTD 484

Query: 553 DVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLALCVLKKDVNATEEQVL 612
           DVINVAGHR+S GA+EE +  H  V +CAVVG  DP+KG +PL L VL          V+
Sbjct: 485 DVINVAGHRLSTGAMEEVLAEHPDVAECAVVGVADPMKGQLPLGLLVLNAGAERATADVV 544

Query: 613 EEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNGKPYKVTPTIEDPSIF 672
            E ++ VR  IGPVAAF+    V++LPKTRSGKI R T+ ++ +G+P+K+  TI+DP I 
Sbjct: 545 RESLQLVRDKIGPVAAFKLCTVVERLPKTRSGKILRGTMRSIADGEPWKMPATIDDPVIL 604

Query: 673 GHIEEVLK 680
             I E L+
Sbjct: 605 DEITEALR 612


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: 1316
Number of extensions: 72
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: 683
Length of database: 618
Length adjustment: 38
Effective length of query: 645
Effective length of database: 580
Effective search space:   374100
Effective search space used:   374100
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