GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Salinicoccus carnicancri Crm

Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate WP_017549722.1 C792_RS0112120 branched-chain amino acid aminotransferase

Query= SwissProt::O31461
         (356 letters)



>NCBI__GCF_000330705.1:WP_017549722.1
          Length = 355

 Score =  414 bits (1064), Expect = e-120
 Identities = 205/356 (57%), Positives = 257/356 (72%), Gaps = 1/356 (0%)

Query: 1   MNKLIEREKTVYYKEKPDPSSLGFGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPSS 60
           M++ ++ E+    K KPD S++ FG  FTDYMF   Y    GW    I PY  L L PS+
Sbjct: 1   MSQTLQIERANELKHKPDVSTVQFGTVFTDYMFTNRYTPEYGWSGASIVPYQNLQLSPSA 60

Query: 61  SVFHYGQAVFEGLKAYRTDDGRVLLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQLV 120
              HYGQ+VFEGLKAY+  D  +LLFRPDQN KR+N S  R+SMP ++EE  L AL +L+
Sbjct: 61  QAIHYGQSVFEGLKAYKQGDD-ILLFRPDQNFKRMNESLSRLSMPEINEENALNALYELL 119

Query: 121 ELEKDWVPKEKGTSLYIRPFVIATEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRIY 180
           ++E+DWVP  +G SLYIRPFV A EP LGV+ S +Y F I+LSPVG YYG  QL P  IY
Sbjct: 120 KVERDWVPDGEGQSLYIRPFVFADEPFLGVRPSETYQFNIILSPVGGYYGATQLNPTSIY 179

Query: 181 VEDEYVRAVNGGVGFAKTAGNYAASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNIF 240
           VED++VR+V GGVGFAK +GNYAASL AQ+KANELGY+QVLWLD +E+KYVEEVGSMNIF
Sbjct: 180 VEDDFVRSVRGGVGFAKVSGNYAASLLAQKKANELGYEQVLWLDGVEQKYVEEVGSMNIF 239

Query: 241 FVINGEAVTPALSGSILSGVTRASAIELIRSWGIPVREERISIDEVYAASARGELTEVFG 300
           FV +GE +TP L+GSIL G+TR S IEL +  G  V+EE+I ID++      G +TEVFG
Sbjct: 240 FVRDGELITPQLNGSILPGITRKSIIELAKHKGYTVKEEKIHIDDLVEDIHGGRVTEVFG 299

Query: 301 TGTAAVVTPVGELNIHGKTVIVGDGQIGDLSKKLYETITDIQLGKVKGPFNWTVEV 356
            GTAAV+ PVG+LNIHG   IV D Q+G++S  L+  +TDIQ G+ + PF W V +
Sbjct: 300 AGTAAVIAPVGKLNIHGIDYIVNDNQVGEVSLDLFNDLTDIQYGRKEDPFGWVVRL 355


Lambda     K      H
   0.317    0.137    0.400 

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: 463
Number of extensions: 11
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: 356
Length of database: 355
Length adjustment: 29
Effective length of query: 327
Effective length of database: 326
Effective search space:   106602
Effective search space used:   106602
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_017549722.1 C792_RS0112120 (branched-chain amino acid aminotransferase)
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01123.hmm
# target sequence database:        /tmp/gapView.2386735.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01123  [M=313]
Accession:   TIGR01123
Description: ilvE_II: branched-chain amino acid aminotransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-124  399.6   0.0   4.5e-124  399.4   0.0    1.0  1  NCBI__GCF_000330705.1:WP_017549722.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017549722.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.4   0.0  4.5e-124  4.5e-124       1     313 []      43     355 .]      43     355 .] 0.98

  Alignments for each domain:
  == domain 1  score: 399.4 bits;  conditional E-value: 4.5e-124
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W+ a ++++++l+l+++++++hYgq vfeGlkay++ d  illfRpd+n kR+++s +rl++Pe++ee  l+a
  NCBI__GCF_000330705.1:WP_017549722.1  43 WSGASIVPYQNLQLSPSAQAIHYGQSVFEGLKAYKQGD-DILLFRPDQNFKRMNESLSRLSMPEINEENALNA 114
                                           999********************************988.7********************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgg.lapvsifveteyvR 145
                                           l +l+k+++dwvp+ + ++sLY+RPf++a e+ lGv+++++y f +++sPvG Y+    l+p+si+ve+++vR
  NCBI__GCF_000330705.1:WP_017549722.1 115 LYELLKVERDWVPDGE-GQSLYIRPFVFADEPFLGVRPSETYQFNIILSPVGGYYGATqLNPTSIYVEDDFVR 186
                                           *************666.9*************************************87669************* PP

                             TIGR01123 146 aapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLeg 218
                                           ++ +G+G++kv+GnYaasllaqkka+e g+++v++ld ve+k++eevG++nif++ + gel+t++l +siL+g
  NCBI__GCF_000330705.1:WP_017549722.1 187 SVRGGVGFAKVSGNYAASLLAQKKANELGYEQVLWLDGVEQKYVEEVGSMNIFFVRD-GELITPQLNGSILPG 258
                                           ******************************************************976.9************** PP

                             TIGR01123 219 vtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtk 289
                                           +tr+s++elak+ g++v+e++i+id+l +  + G +  vf++Gtaavi+Pvg+l+i+g  ++v++++vGev+ 
  NCBI__GCF_000330705.1:WP_017549722.1 259 ITRKSIIELAKHKGYTVKEEKIHIDDLVEDIHGGRVteVFGAGTAAVIAPVGKLNIHGIDYIVNDNQVGEVSL 331
                                           **********************************9999*********************************** PP

                             TIGR01123 290 klrdeltdiqyGkledkegWivev 313
                                            l++ ltdiqyG++ed++gW+v++
  NCBI__GCF_000330705.1:WP_017549722.1 332 DLFNDLTDIQYGRKEDPFGWVVRL 355
                                           *********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (355 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 14.78
//
[ok]

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