GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Phyllobacterium endophyticum PEPV15

Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_106718644.1 CU100_RS19210 thiamine pyrophosphate-binding protein

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_003010935.1:WP_106718644.1
          Length = 550

 Score =  251 bits (640), Expect = 7e-71
 Identities = 164/537 (30%), Positives = 264/537 (49%), Gaps = 22/537 (4%)

Query: 3   GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATG 62
           G + +V AL A  V  +F  PG + + V DALYD G+   +CR E GAAM A  + + TG
Sbjct: 4   GGELIVEALAANQVERLFCVPGESYLAVLDALYDTGIGVTVCRAEGGAAMMAEAWGKLTG 63

Query: 63  KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACT 122
           K G+C  T GPGATN   G+  A  DS P++   GQV       +AFQEV+         
Sbjct: 64  KPGICFVTRGPGATNASPGIHIARQDSTPLILFIGQVQRDAREREAFQEVEYRRFFANTA 123

Query: 123 KHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDI---QLASGDLEPWFTTVENEV 179
           K    +     +P  +  AF VA SGRPGPV++ +P+D+   ++ +   + W      E 
Sbjct: 124 KWVAEIDDARRIPEFVTRAFSVATSGRPGPVVLALPEDMLTDKVEAVAAQGWQPV---ET 180

Query: 180 TFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEA 239
               A +E+   +L  A KP + +GG      AV ++  F     +P  C+ +     + 
Sbjct: 181 GPSPACIEKLADLLQGATKPFMILGGSRWSEHAVRSITRFAEKWHLPVGCSFRRQMLFDH 240

Query: 240 DYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTG---KLNTFAPHASVIHMDID 296
            +P Y G +G+    A    V+E D+L+ VG RF +  +     +++  P  ++IH+  D
Sbjct: 241 LHPNYAGDVGIGINPALATRVKEADVLLLVGGRFGEMPSSGYTLIDSPYPKQTLIHVYPD 300

Query: 297 PAEMNKLRQAHVALQGDLNALLPALQQ--PLNQYDWQQHCAQLRDEH-SWR---YDHPGD 350
             E+ ++ +  +A+    +    A++   P +  +W        + + +W       PG+
Sbjct: 301 ADELGRVYRPSLAINSAPDTFAEAVEHLAPPSHINWPGEAETAHESYLAWSTPPKTGPGE 360

Query: 351 AIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSG--LGTMGFGLP 408
               P ++  L    P D ++T   G +  W   H  H R   F T +    G+MG+GLP
Sbjct: 361 VAMGP-IMSYLESVLPEDAIMTNGAGNYATWL--HRFH-RFRRFGTQAAPTSGSMGYGLP 416

Query: 409 AAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLF 468
           AAV A+   P   V+C +GDG F+MN Q+  T  +  LP+ +++++N   G +R  Q+  
Sbjct: 417 AAVAAKQLNPERMVICFAGDGCFLMNGQDFATAVKYGLPIIVLVINNNIYGTIRMHQERE 476

Query: 469 FQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525
           +  R S T LT NPDF MLA A+G HG+ +   ++ E A    + S  P ++ + +D
Sbjct: 477 YPGRVSATDLT-NPDFAMLARAYGGHGETVAATEEFEGAWQRAVESGKPAIIEIQLD 532


Lambda     K      H
   0.320    0.135    0.410 

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: 769
Number of extensions: 37
Number of successful extensions: 4
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: 548
Length of database: 550
Length adjustment: 36
Effective length of query: 512
Effective length of database: 514
Effective search space:   263168
Effective search space used:   263168
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 26 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