Alignments for a candidate for hisC in Methylobacterium sp. 4-46 Apr-46

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Methylobacterium sp. 4-46 Apr-46

Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate WP_012334967.1 M446_RS25345 histidinol-phosphate transaminase

Query= reanno::azobra:AZOBR_RS20485
         (364 letters)



>NCBI__GCF_000019365.1:WP_012334967.1
          Length = 370

 Score =  365 bits (936), Expect = e-105
 Identities = 189/360 (52%), Positives = 246/360 (68%), Gaps = 7/360 (1%)

Query: 8   PAPRPGILDIAPYVGGEHAGHI-----RLASNEGALGPSPRAVEAYRAAAGELHRYPDGG 62
           P PRPG+L I  YV G+ A        +L+SNE  LGPSP AV A R  A  L  YPDG 
Sbjct: 7   PVPRPGVLAIEAYVPGKSAAPAGVKLHKLSSNETPLGPSPAAVAAMRETASHLELYPDGS 66

Query: 63  SAKLRKAIAERFGLDADRVVCGAGSDELIALLIRAYAGPGDEVLYSQHGFLMYPIGAKSV 122
           +A LR+AIA ++GLD  R+VCGAGSDEL++LL  A+ GPGDE +YS++GFL+Y I   + 
Sbjct: 67  AAALRRAIAGKYGLDPARIVCGAGSDELLSLLTYAFMGPGDEGIYSEYGFLVYRIAILAA 126

Query: 123 GATPVQAPETNLTTDVDSLLAHVTPRTRLVFVANPNNPTGTYITADEMARLHAGLPENAI 182
           G TPV APE + T DVD++LA VTPRTR+V++ANPNNPTGTY+  DE+ RLHAGLP + +
Sbjct: 127 GGTPVVAPERDHTADVDAILAAVTPRTRIVYLANPNNPTGTYLPFDEVRRLHAGLPGDVL 186

Query: 183 LVIDAAYAEYMNHNDYSAGQELVDRFPNVVMTRTFSKIFALGSVRLGWAYCPAGIADVLN 242
           LV+DAAYAEY+  NDY+AG ELV    NVVMTRTFSK + L ++R+GW   P  +AD +N
Sbjct: 187 LVLDAAYAEYVRRNDYAAGLELVAESENVVMTRTFSKAYGLAALRIGWMVAPPAVADAVN 246

Query: 243 RVRGPFNVSSAAQIAGVAALEDTAFLERSRSHNIEWREWFVQQVHGLGLKTHPSVTNFVL 302
           R+RGPFN+ S A  AG AA+ D A +  + +HN EW     + +  +GL   PSV NFVL
Sbjct: 247 RIRGPFNLGSPAIAAGAAAVADDAHIAAAVAHNEEWLPKVTRALTEIGLSVTPSVGNFVL 306

Query: 303 VDFAGQTAGKDDAEAARLFLKGRGILVRQMPAYGLPSCLRVTIGTEAEMREVVQALKDFL 362
           + F     G+  AE A  FL  RG+++R++ AYGLP  LR+TIG+      V+ AL+ F+
Sbjct: 307 IHFP-DAPGRGAAE-ADAFLTARGLILRRVAAYGLPHALRMTIGSAEANEAVIAALRAFV 364


Lambda     K      H
   0.319    0.136    0.405 

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: 447
Number of extensions: 15
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: 364
Length of database: 370
Length adjustment: 30
Effective length of query: 334
Effective length of database: 340
Effective search space:   113560
Effective search space used:   113560
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: 49 (23.5 bits)

Align candidate WP_012334967.1 M446_RS25345 (histidinol-phosphate transaminase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.3795225.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.8e-88  281.6   0.0    4.3e-88  281.5   0.0    1.0  1  NCBI__GCF_000019365.1:WP_012334967.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019365.1:WP_012334967.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.5   0.0   4.3e-88   4.3e-88       1     348 [.      10     362 ..      10     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: 281.5 bits;  conditional E-value: 4.3e-88
                             TIGR01141   1 rekikklepYqpgarelgek.evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgvee 72 
                                           r+ + ++e+Y+pg+++ +   +  kL+snE P+gps+++++a++e++++l++Ypd +a++l++a+a ++g+++
  NCBI__GCF_000019365.1:WP_012334967.1  10 RPGVLAIEAYVPGKSAAPAGvKLHKLSSNETPLGPSPAAVAAMRETASHLELYPDGSAAALRRAIAGKYGLDP 82 
                                           5678899******66655555799************************************************* PP

                             TIGR01141  73 enillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvk 145
                                           + i+ g+Gsdel++ll+ af+ pgd+ +++e+ + +Y++   +ag   + +p +++ + d++a+l+a++ +++
  NCBI__GCF_000019365.1:WP_012334967.1  83 ARIVCGAGSDELLSLLTYAFMGPGDEGIYSEYGFLVYRIAILAAGGTPVVAPERDH-TADVDAILAAVTPRTR 154
                                           ***************************************99999888888887777.59************** PP

                             TIGR01141 146 lvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlSKafgL 214
                                           +v+la+PnnPtG++l  +e++++ +    d+l V+D AY e+ ++   a  lel+ae +n+v++rT+SKa+gL
  NCBI__GCF_000019365.1:WP_012334967.1 155 IVYLANPNNPTGTYLPFDEVRRLHAGLpGDVLLVLDAAYAEYVRRndyAAGLELVAESENVVMTRTFSKAYGL 227
                                           ***************************77**************998888899********************* PP

                             TIGR01141 215 AglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevye 287
                                           A+lR+G ++a +++++a++++r p+n+ s+a +a+ aa+ d+++i++ v+++++    ++ +l+++ gl+v +
  NCBI__GCF_000019365.1:WP_012334967.1 228 AALRIGWMVAPPAVADAVNRIRGPFNLGSPAIAAGAAAVADDAHIAAAVAHNEEWLPKVTRALTEI-GLSVTP 299
                                           ******************************************************************.8***** PP

                             TIGR01141 288 SkaNFvlikvke....daeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                           S +NFvli+++      a+e+   l+ +g+i+R ++++ gl +++lR+t+G++e ne++++al+ 
  NCBI__GCF_000019365.1:WP_012334967.1 300 SVGNFVLIHFPDapgrGAAEADAFLTARGLILRRVAAY-GL-PHALRMTIGSAEANEAVIAALRA 362
                                           ***********987766677777799**********99.85.********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (370 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 30.11
//
[ok]

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:

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