Alignments for a candidate for ilvE in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Saccharomonospora cyanea NA-134

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_043537101.1 SACCYDRAFT_RS06020 branched-chain amino acid aminotransferase

Query= BRENDA::A0R066
         (368 letters)



>NCBI__GCF_000244975.1:WP_043537101.1
          Length = 367

 Score =  504 bits (1298), Expect = e-147
 Identities = 245/363 (67%), Positives = 292/363 (80%), Gaps = 2/363 (0%)

Query: 6   LEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDP 65
           + F+ S +T PA+      +LA PGFG ++TDHM ++ +T   GWH+A++  Y P+ LDP
Sbjct: 5   IPFSHSPSTRPASAERVAEVLAKPGFGVHFTDHMATVKWTKGTGWHDAELRAYEPVSLDP 64

Query: 66  SAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQ 125
           +  VLHYGQ IFEGLKAYR  DG++ +FRP+ NAAR + SARRLA+PELP+E+F+ S+R+
Sbjct: 65  ATAVLHYGQAIFEGLKAYRQPDGTVKAFRPDVNAARFRRSARRLAMPELPDELFLGSIRE 124

Query: 126 LIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVR-PSNEYRYLLIASPAGAYFKGGIKPV 184
           LIA DE+WVP   G+ SLYLRPF+IATE GLGV  PS+ Y Y+LIASPAG+YF GG+KPV
Sbjct: 125 LIAADERWVPTRQGD-SLYLRPFLIATEAGLGVNSPSSSYLYMLIASPAGSYFTGGVKPV 183

Query: 185 SVWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGM 244
           SVWLS EYVRA+PGGTG AK  GNYAAS +AQAQA E GCDQVVWLDA ERRYVEEMGGM
Sbjct: 184 SVWLSTEYVRAAPGGTGEAKCAGNYAASFVAQAQAVEQGCDQVVWLDANERRYVEEMGGM 243

Query: 245 NLFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAG 304
           NLFFVFGSG  AR+VTPELSGSLLPG+TRDSLL+LA+D G+ VEER+I  DEW+K A +G
Sbjct: 244 NLFFVFGSGSDARVVTPELSGSLLPGVTRDSLLRLASDFGYRVEERRITTDEWEKTASSG 303

Query: 305 EITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGWM 364
           E+TEVFACGTAAVITPV HVKH  GEF++ DG PGEITM LR+ LTGIQ GT  D HGWM
Sbjct: 304 ELTEVFACGTAAVITPVGHVKHAGGEFSVGDGSPGEITMKLREELTGIQEGTRPDPHGWM 363

Query: 365 ARL 367
             L
Sbjct: 364 YTL 366


Lambda     K      H
   0.318    0.135    0.409 

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: 545
Number of extensions: 19
Number of successful extensions: 3
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: 368
Length of database: 367
Length adjustment: 30
Effective length of query: 338
Effective length of database: 337
Effective search space:   113906
Effective search space used:   113906
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: 49 (23.5 bits)

Align candidate WP_043537101.1 SACCYDRAFT_RS06020 (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.17447.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-138  446.7   0.0   2.1e-138  446.5   0.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_043537101.1  SACCYDRAFT_RS06020 branched-chai


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_043537101.1  SACCYDRAFT_RS06020 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.5   0.0  2.1e-138  2.1e-138       1     312 [.      49     365 ..      49     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 446.5 bits;  conditional E-value: 2.1e-138
                                 TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 
                                               W++ael+++++++ld+++avlhYgq++feGlkayR+ dG +  fRpd na+R+rrsa+rl++Pel++el
  lcl|NCBI__GCF_000244975.1:WP_043537101.1  49 WHDAELRAYEPVSLDPATAVLHYGQAIFEGLKAYRQPDGTVKAFRPDVNAARFRRSARRLAMPELPDEL 117
                                               ********************************************************************* PP

                                 TIGR01123  70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvk.aakeylflvlasPvGaYfkgglapvsi 137
                                               fl ++++l++ad++wvp+ + + sLYlRPfliate+ lGv+ ++++yl++++asP+G+Yf gg++pvs+
  lcl|NCBI__GCF_000244975.1:WP_043537101.1 118 FLGSIRELIAADERWVPTRQ-GDSLYLRPFLIATEAGLGVNsPSSSYLYMLIASPAGSYFTGGVKPVSV 185
                                               *****************887.9******************73577************************ PP

                                 TIGR01123 138 fveteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdg.. 204
                                               +++teyvRaap+GtG +k++GnYaas+ aq++a eqg+d+vv+ld++e++++ee+G++n+f++ ++g  
  lcl|NCBI__GCF_000244975.1:WP_043537101.1 186 WLSTEYVRAAPGGTGEAKCAGNYAASFVAQAQAVEQGCDQVVWLDANERRYVEEMGGMNLFFVFGSGsd 254
                                               ****************************************************************99987 PP

                                 TIGR01123 205 .elvttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgel 270
                                                ++vt++ls+s+L+gvtr+sll+la d g++veer+i+ de+++++ +Ge+  vfacGtaavitPvg++
  lcl|NCBI__GCF_000244975.1:WP_043537101.1 255 aRVVTPELSGSLLPGVTRDSLLRLASDFGYRVEERRITTDEWEKTASSGELteVFACGTAAVITPVGHV 323
                                               789***********************************************999**************** PP

                                 TIGR01123 271 kiegkevevkseevGevtkklrdeltdiqyGkledkegWive 312
                                               k+ g e++v ++ +Ge+t+klr+elt+iq G+  d++gW+  
  lcl|NCBI__GCF_000244975.1:WP_043537101.1 324 KHAGGEFSVGDGSPGEITMKLREELTGIQEGTRPDPHGWMYT 365
                                               ***************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (367 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.36
//
[ok]

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

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