Aligments for a candidate for acs in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments 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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, or view the source code.

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