Alignments for a candidate for prpE in Amycolatopsis halophila YIM 93223

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Amycolatopsis halophila YIM 93223

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_034269395.1 AMYHA_RS07525 propionyl-CoA synthetase

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



>NCBI__GCF_000504245.1:WP_034269395.1
          Length = 626

 Score =  800 bits (2067), Expect = 0.0
 Identities = 384/622 (61%), Positives = 466/622 (74%), Gaps = 1/622 (0%)

Query: 2   SYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRH 61
           +Y+EVY+   A+PE FW+ AAE I W  APTKAL D    LY WF D  +NT YNA+DRH
Sbjct: 3   AYAEVYDRSLADPEGFWLAAAEDIDWTRAPTKALDDGRAPLYRWFPDGELNTAYNALDRH 62

Query: 62  VEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPE 121
           VE GRGEQ A+IYDSP+T TK   +Y+ELR+ VA +AGAL + GV KGDRVIIYMPM+PE
Sbjct: 63  VEAGRGEQPALIYDSPVTDTKTSYTYLELRDYVAIVAGALSSLGVGKGDRVIIYMPMVPE 122

Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDG 181
           A+ AMLACARLGA+HSVVFGGFA  ELA R+DDA P  I+AASCG+EP R V YKP+++ 
Sbjct: 123 AIIAMLACARLGAIHSVVFGGFAPKELAARVDDAQPTVIVAASCGIEPTRVVEYKPIIED 182

Query: 182 AIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSG 241
           A+   TH+PD  V+ QR+   AE+ E RDV+WH       P + VPV    P YILYTSG
Sbjct: 183 ALATTTHQPDHVVMLQRQTATAEMTE-RDVDWHDLVASASPVDPVPVAATDPLYILYTSG 241

Query: 242 TTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNT 301
           TTG+PKGV+R T G  VAL W+M+NIY+V PGDV+W ASDVGWVVGHSYI YGPL+ G T
Sbjct: 242 TTGKPKGVVRDTGGHAVALAWSMRNIYDVAPGDVWWTASDVGWVVGHSYIVYGPLLIGAT 301

Query: 302 TIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQV 361
           T+++EGKP+GTPDAG FWRVISEH+ K+ FTAPTA RA+K+ DPK   V KYDLS  + +
Sbjct: 302 TVLYEGKPVGTPDAGAFWRVISEHRAKALFTAPTALRAIKKIDPKASEVAKYDLSAFETL 361

Query: 362 YLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGY 421
           +LAGER DP+T  WA + L VPVIDHWWQTETGW IAANP G+E LP K GS  VP+PGY
Sbjct: 362 FLAGERLDPETYHWAHDTLGVPVIDHWWQTETGWPIAANPRGLETLPVKPGSATVPVPGY 421

Query: 422 TVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGM 481
            + +LD+ G+ V  G+ GAIA+KLPLPPGTL TLW  +DR+ +SYL+ + GYY TGD+G 
Sbjct: 422 DIQVLDQRGNQVPAGQEGAIAIKLPLPPGTLLTLWGDDDRYVESYLSRYEGYYLTGDSGY 481

Query: 482 KDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFL 541
            D DGYL++M RTDDVINVAGHRLSTG++E  LA HP VAECAVIGV D LKGQ P GF+
Sbjct: 482 LDADGYLFVMGRTDDVINVAGHRLSTGSIEAALASHPAVAECAVIGVHDELKGQVPRGFV 541

Query: 542 CLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGT 601
            L +G D     +  ++V+ VR  +GPVAAF+   VVD LPKTRSGKILR TM  IADG 
Sbjct: 542 VLKSGVDVEESTLHDELVEAVRRDVGPVAAFRDVSVVDALPKTRSGKILRKTMRGIADGR 601

Query: 602 DWKMPATIDDPAILDEITTALQ 623
           D  +P+TI+D  +LD +   L+
Sbjct: 602 DEPVPSTIEDVGVLDSLRAVLR 623


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: 1364
Number of extensions: 75
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: 626
Length adjustment: 38
Effective length of query: 591
Effective length of database: 588
Effective search space:   347508
Effective search space used:   347508
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:

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
the source code
instructions for running GapMind on your computer

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