GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Desulfatibacillum aliphaticivorans DSM 15576

Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_028316428.1 G491_RS0124505 propionyl-CoA synthetase

Query= metacyc::MONOMER-21334
         (629 letters)



>NCBI__GCF_000429905.1:WP_028316428.1
          Length = 639

 Score =  847 bits (2188), Expect = 0.0
 Identities = 400/627 (63%), Positives = 480/627 (76%)

Query: 2   AYQDVYESWKSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDRH 61
           AY + Y     +PE FW   A+   W E   + LDDSN P Y WF+    NTC+NA+D H
Sbjct: 4   AYDEAYRESLENPEEFWGRHAEECFWYEKWDKVLDDSNKPFYRWFSGGVTNTCYNALDMH 63

Query: 62  VEAGRGEQTAIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIPE 121
           VE G G++ A+IYDSP+T+T ++ +Y ELR+ VA+ AG L   GVEKGDRV++YMPMI E
Sbjct: 64  VEKGAGDRVALIYDSPVTNTIKKYTYAELRDEVALFAGVLAEYGVEKGDRVVLYMPMIAE 123

Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLDG 181
           A  AMLACARLGAVHSVVFGGFAANELA RI+DA+PKAI++ASCG+E  +V+ YKPLLD 
Sbjct: 124 AAIAMLACARLGAVHSVVFGGFAANELATRINDARPKAIVSASCGIEGKKVIPYKPLLDA 183

Query: 182 AIDMAKHKPEFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTSG 241
           AI++++HKP+ C+I QR  E A +   RD +W        P +CVPV    P YILYTSG
Sbjct: 184 AIEISEHKPKNCMILQRPMETADMHPSRDVDWTEAMKKASPKDCVPVLATDPLYILYTSG 243

Query: 242 TTGAPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNT 301
           TTG PKGV+R   GH+VAL W+MK +Y+VD GDV+WAASDVGWVVGHSYI Y PL  G T
Sbjct: 244 TTGQPKGVVRDNGGHMVALKWSMKAVYDVDEGDVWWAASDVGWVVGHSYIVYAPLFKGCT 303

Query: 302 TIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDPKGEMLAKYDLSHLKAL 361
           TI+FEGKPVGTPDAG FWRVISEHKVK  FTAPTA RA+KREDP   ++  YDLS+ K L
Sbjct: 304 TILFEGKPVGTPDAGVFWRVISEHKVKCMFTAPTAYRAIKREDPGAALMKNYDLSNFKIL 363

Query: 362 YLAGERADPDTIIWAQKALSVPVIDHWWQTETGWTIAGNPLGIEELPTKLGSPAKAMPGY 421
           +LAGER+DPDTI W+++ L VPVIDHWWQTETGW IA N +G+   P K GSP KA+PG+
Sbjct: 364 FLAGERSDPDTITWSERNLGVPVIDHWWQTETGWAIAANCMGLHHFPVKYGSPTKAVPGW 423

Query: 422 DVQILDEGGHQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYYETGDAGM 481
           +VQ+LDE G    PG++GA+ VKLPLPPGTLP LW  +  F   YL  F GYY T DAG 
Sbjct: 424 NVQVLDEMGRPAAPGQIGALVVKLPLPPGTLPTLWGNDQAFVNKYLRDFDGYYTTADAGY 483

Query: 482 IDEDGYLYIMARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKGQMPLGFL 541
           IDEDGY+Y+MARTDD+INVAGHRLSTG MEEVLA H DVAECAV+GV D LKGQ+PLGFL
Sbjct: 484 IDEDGYIYVMARTDDIINVAGHRLSTGAMEEVLADHPDVAECAVLGVEDPLKGQLPLGFL 543

Query: 542 CLNNGCNRDHGDVVKEVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGTMVSIADGK 601
            LN G  R + ++VKEVV+++R++IGPV+AFK A VVDRLPKTRSGKILRG M  IAD K
Sbjct: 544 VLNAGVTRSNDEIVKEVVEMIRERIGPVSAFKTATVVDRLPKTRSGKILRGVMRQIADNK 603

Query: 602 EYKMPATIDDPAILDEIKVALQSLGYA 628
            Y+MPATIDDP+IL EI+ AL ++GYA
Sbjct: 604 SYRMPATIDDPSILKEIENALNTIGYA 630


Lambda     K      H
   0.319    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: 1397
Number of extensions: 65
Number of successful extensions: 1
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: 639
Length adjustment: 38
Effective length of query: 591
Effective length of database: 601
Effective search space:   355191
Effective search space used:   355191
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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