GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Marinobacter adhaerens HP15

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate GFF2099 HP15_2053 PrpE protein

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



>FitnessBrowser__Marino:GFF2099
          Length = 624

 Score =  755 bits (1950), Expect = 0.0
 Identities = 352/619 (56%), Positives = 455/619 (73%)

Query: 1   MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDR 60
           M Y   +      P++FW E AE I W   P        +G  +WF D  +NTC  A+D 
Sbjct: 1   MDYHSEFRRSIDKPDEFWREQAEKIDWIEPPKTIWQPTDNGHGQWFPDGTLNTCDVALDA 60

Query: 61  HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120
           ++  GRG+Q A+IYDSP+T T+R  +Y EL + VA  AGAL+ +G+ KGDRVIIYMPMIP
Sbjct: 61  NIRAGRGDQKALIYDSPVTDTQRSYTYNELTDEVARFAGALKDRGITKGDRVIIYMPMIP 120

Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180
           EA+ AML CAR+GA+HSVVFGGFAA+ELAVRIDDA PKA+I ASCG+E  R + YKPL+D
Sbjct: 121 EAVIAMLGCARIGAIHSVVFGGFAAHELAVRIDDAKPKAVITASCGIEVTRVIEYKPLVD 180

Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTS 240
            AID A+HKP+ C+++QR+Q  AEL   RD +W+      EPA+ VPV+   P YILYTS
Sbjct: 181 KAIDQASHKPETCIVYQRQQVQAELQACRDHDWNELMETAEPADPVPVKSTDPLYILYTS 240

Query: 241 GTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300
           GTTG+PKGV+R   G  VALN++MK +Y+  PGDV+WAASDVGWVVGHSYI Y PL  G 
Sbjct: 241 GTTGKPKGVVRDNGGHAVALNYSMKLVYDAKPGDVYWAASDVGWVVGHSYIVYAPLFAGC 300

Query: 301 TTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQ 360
           TTI++EGKP+ TPDAG FWRV+ +HKV   FTAPTAFRAV++EDP+ + + +YD+S LK+
Sbjct: 301 TTIMYEGKPVKTPDAGAFWRVVQDHKVNMLFTAPTAFRAVRKEDPEADQLSRYDISSLKR 360

Query: 361 VYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPG 420
           ++LAGER DP T  W +E   +PV+DHWWQTETGW+I  NP+GIE + TK GS  VP PG
Sbjct: 361 LFLAGERLDPATYEWLKEHTGLPVLDHWWQTETGWAICCNPVGIELMATKPGSATVPSPG 420

Query: 421 YTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAG 480
           Y V ++D  G  +  GE G IAVKLPLPPG + T+W  ++RF+K+YL    G+Y +GD G
Sbjct: 421 YNVQVVDMNGSQMPAGEQGQIAVKLPLPPGCMMTVWGDDERFRKTYLEPISGFYSSGDGG 480

Query: 481 MKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGF 540
             D+DGY+++M RTDDVINVAGHRLSTG MEEV+A HP +AEC V+G  D +KGQ P+G 
Sbjct: 481 FIDDDGYVFVMGRTDDVINVAGHRLSTGEMEEVVASHPAIAECCVVGAHDDMKGQIPIGL 540

Query: 541 LCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600
           + +  G    H+++  ++V++VR+KIG +A F+ A VVDRLPKTRSGKILR  +  IADG
Sbjct: 541 VLIKDGATIDHDELEDELVEMVRDKIGAIACFRRALVVDRLPKTRSGKILRRVIRQIADG 600

Query: 601 TDWKMPATIDDPAILDEIT 619
            ++ +P+TIDDPAIL+EI+
Sbjct: 601 EEYSVPSTIDDPAILEEIS 619


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: 1336
Number of extensions: 58
Number of successful extensions: 2
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: 624
Length adjustment: 38
Effective length of query: 591
Effective length of database: 586
Effective search space:   346326
Effective search space used:   346326
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 Aug 03 2021. The underlying query database was built on Aug 03 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