Alignments for a candidate for ilvE in Geobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Geobacter lovleyi SZ

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_012470683.1 GLOV_RS13060 branched-chain amino acid aminotransferase

Query= SwissProt::P39576
         (363 letters)



>NCBI__GCF_000020385.1:WP_012470683.1
          Length = 359

 Score =  382 bits (981), Expect = e-111
 Identities = 185/345 (53%), Positives = 242/345 (70%)

Query: 14  KKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFEG 73
           K+   D  QL FGR+FTD M ++++ ADKGW++ RI PY+P  +DPA  V HY Q +FEG
Sbjct: 14  KQKVADETQLGFGRLFTDRMLLVEWTADKGWHNARIKPYEPFMLDPATTVLHYAQEIFEG 73

Query: 74  LKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAEG 133
           LKAY  +D  + LFRPE N  R NQS  R+C+P++ EE  L+G+ +LV ++KDWIP+A G
Sbjct: 74  LKAYKWDDGRIALFRPEMNARRFNQSASRMCMPEVPEELFLDGIDKLVELEKDWIPSAPG 133

Query: 134 TSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVRAVKGGT 193
           T++YIRP +IA +P+LGV     Y   +ILSPVG+YY  G  PV I VE ++VR+V GGT
Sbjct: 134 TAMYIRPAMIAVDPYLGVKPGDHYYFFVILSPVGAYYAAGFNPVSILVEDKYVRSVAGGT 193

Query: 194 GNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKINGEIVTPMLN 253
           G+AKT GNYASSLKA   A++KGF QVLWLDG E++YIEEVG+MN+FF     IVT  L 
Sbjct: 194 GDAKTGGNYASSLKAGLEAKKKGFDQVLWLDGKERRYIEEVGAMNMFFAYGNHIVTAPLT 253

Query: 254 GSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPVGEL 313
           GSIL GITR SV+ L    G  V ER I +DE+    ++G + EAFG+GTAAV++PVG L
Sbjct: 254 GSILSGITRESVLRLAIELGCTVEERLIDVDELFADLRNGKVTEAFGSGTAAVVTPVGTL 313

Query: 314 IWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEVAA 358
            ++DE L + +G  G I +KLYD +TGIQ G + D +GW   V A
Sbjct: 314 GYKDEALQVGDGGVGAITQKLYDALTGIQTGKLDDRYGWIRIVDA 358


Lambda     K      H
   0.316    0.135    0.390 

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: 460
Number of extensions: 21
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: 363
Length of database: 359
Length adjustment: 29
Effective length of query: 334
Effective length of database: 330
Effective search space:   110220
Effective search space used:   110220
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_012470683.1 GLOV_RS13060 (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.16669.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-127  409.5   0.0   4.6e-127  409.3   0.0    1.0  1  lcl|NCBI__GCF_000020385.1:WP_012470683.1  GLOV_RS13060 branched-chain amin


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012470683.1  GLOV_RS13060 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.3   0.0  4.6e-127  4.6e-127       1     311 [.      44     354 ..      44     356 .. 0.99

  Alignments for each domain:
  == domain 1  score: 409.3 bits;  conditional E-value: 4.6e-127
                                 TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 
                                               W++a++++++++ ld++++vlhY+qe+feGlkay+++dG+i lfRp+ na+R+++sa+r+ +Pe++eel
  lcl|NCBI__GCF_000020385.1:WP_012470683.1  44 WHNARIKPYEPFMLDPATTVLHYAQEIFEGLKAYKWDDGRIALFRPEMNARRFNQSASRMCMPEVPEEL 112
                                               ********************************************************************* PP

                                 TIGR01123  70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138
                                               fl+ + +lv+++kdw+p+a  ++++Y+RP +ia++++lGvk+  +y f+v++sPvGaY++ g +pvsi+
  lcl|NCBI__GCF_000020385.1:WP_012470683.1 113 FLDGIDKLVELEKDWIPSAP-GTAMYIRPAMIAVDPYLGVKPGDHYYFFVILSPVGAYYAAGFNPVSIL 180
                                               *****************999.9*********************************************** PP

                                 TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207
                                               ve++yvR++ +GtG +k+gGnYa+sl+a  +a+++g+d+v++ld +e+++ieevGa+n+f+ +++ ++v
  lcl|NCBI__GCF_000020385.1:WP_012470683.1 181 VEDKYVRSVAGGTGDAKTGGNYASSLKAGLEAKKKGFDQVLWLDGKERRYIEEVGAMNMFFAYGN-HIV 248
                                               ****************************************************************8.*** PP

                                 TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274
                                               t pl++siL+g+tres+l+la +lg +veer i++del a   +G++  +f++Gtaav+tPvg l  ++
  lcl|NCBI__GCF_000020385.1:WP_012470683.1 249 TAPLTGSILSGITRESVLRLAIELGCTVEERLIDVDELFADLRNGKVteAFGSGTAAVVTPVGTLGYKD 317
                                               *********************************************9999******************** PP

                                 TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWiv 311
                                               + ++v ++ vG +t+kl+d+lt+iq+Gkl+d++gWi 
  lcl|NCBI__GCF_000020385.1:WP_012470683.1 318 EALQVGDGGVGAITQKLYDALTGIQTGKLDDRYGWIR 354
                                               ***********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (359 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.21
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis