GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Phaeobacter inhibens BS107

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate GFF1175 PGA1_c11900 propionate-CoA ligase PrpE

Query= BRENDA::A0A0G2K047
         (683 letters)



>FitnessBrowser__Phaeo:GFF1175
          Length = 629

 Score =  674 bits (1738), Expect = 0.0
 Identities = 321/614 (52%), Positives = 426/614 (69%), Gaps = 2/614 (0%)

Query: 67  ADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQGDKIA 126
           A+PE+FW +AAE ISW    TK L ++      WF +  +N CYNA+DRH+E G+G++ A
Sbjct: 12  ANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHVEQGRGEQTA 71

Query: 127 IIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAMLACAR 186
           IIYDSP+T TK  ISY E+  +V+ LAG L  +GV+KGD V+IYMPMIP+A+ AMLACAR
Sbjct: 72  IIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEALEAMLACAR 131

Query: 187 IGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQHKPD 246
           +GA+HS++FGGFA+ EL+ RID   PK ++ AS G+EPGR V Y PLL+ A+ +  HKPD
Sbjct: 132 LGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGAIDLATHKPD 191

Query: 247 RLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKGVV 306
             +I+ R   E   L+ GRD++W       +  +CVPV   HP YILYTSGTTG PKGV+
Sbjct: 192 FCVIFQR-EQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSGTTGQPKGVI 250

Query: 307 RPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGKPV 366
           R T G  V LNWTM +IY + PG+V+WAASD+GWVVGHSYICYGPL+HGNTT+++EGKP+
Sbjct: 251 RHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTTIVFEGKPI 310

Query: 367 GTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGERCDV 426
           GTPDAG ++RV++EH V + FTAPTA RA++++DP     K+Y L+  K +++AGER D 
Sbjct: 311 GTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQVYLAGERADP 370

Query: 427 ETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPGYNVMILDDN 486
           +T+ W+++  +VPV+DHWWQTETG  I A+ +G+    T   G     +PGY V ILD+ 
Sbjct: 371 DTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPT-KLGSPAVPMPGYTVDILDEG 429

Query: 487 MQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEEGYLY 546
              +    LG I VKLPLPPG    LW  ++ FK  Y   FPGYY+T DAG  DE+GYLY
Sbjct: 430 GHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGMKDEDGYLY 489

Query: 547 VMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLALCVLKKDVNA 606
           +M+R DDVINVAGHR+S GA+EE +  H  V +CAV+G  D LKG  P+    L    + 
Sbjct: 490 IMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFLCLNAGCDT 549

Query: 607 TEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNGKPYKVTPTI 666
             E V+ ++VK VR+ IGPVAAF+ A  V +LPKTRSGKI R T+  + +G  +K+  TI
Sbjct: 550 PHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGTDWKMPATI 609

Query: 667 EDPSIFGHIEEVLK 680
           +DP+I   I   L+
Sbjct: 610 DDPAILDEITTALQ 623


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: 1356
Number of extensions: 52
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: 629
Length adjustment: 38
Effective length of query: 645
Effective length of database: 591
Effective search space:   381195
Effective search space used:   381195
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 17 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