Alignments for a candidate for hisC in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Herbaspirillum seropedicae SmR1

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9 (characterized, see rationale)
to candidate HSERO_RS20335 HSERO_RS20335 histidinol-phosphate aminotransferase

Query= uniprot:A0A2R7PAQ8
         (373 letters)



>FitnessBrowser__HerbieS:HSERO_RS20335
          Length = 372

 Score =  355 bits (911), Expect = e-102
 Identities = 196/359 (54%), Positives = 251/359 (69%), Gaps = 10/359 (2%)

Query: 15  IRPDVRAMHSYVVQPSTGMLKMDAMENPFRLPAHLQAALGQRLGSVALNRYPGDRIADLK 74
           IRP VR   SY V  + GM+K+DAMENP+ LPA L+  L QRL ++ LNRYP      LK
Sbjct: 21  IRPVVRGWQSYHVPSAEGMVKLDAMENPYLLPAELREQLAQRLAALELNRYPVPSYTALK 80

Query: 75  AALAQYAGMPEGYGIVLGNGSDELITLLALACAQPGTGQRATMLAPMPGFVMYPLSAQLQ 134
           AA+ +  G+P GY ++LGNGSDELITLL++ACAQPG     T+LAP PGFVMY +SA++ 
Sbjct: 81  AAICKGLGVPAGYDVLLGNGSDELITLLSVACAQPG----RTILAPEPGFVMYGVSAKMA 136

Query: 135 GLDFVGVPLTPDFELDEPAMLAAIGQHRPAITYIAYPNNPTATLWDEGAVQRIIDAAGAQ 194
           GL++VGVPL  D  LD PAMLAA+  H+P IT++ YPNNPT TL++   V RI++AA A 
Sbjct: 137 GLEYVGVPLCADLSLDLPAMLAAMEAHKPVITWLGYPNNPTGTLYEMADVLRIVEAA-AP 195

Query: 195 GGIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAGVRLGYLIGPSAFVSE 254
            G+VV+DEAYQPFA+ T    M A P  N +++LMRT+SK GLAG+RLGYL    A + E
Sbjct: 196 YGLVVVDEAYQPFAAST---LMPALPQHN-NLVLMRTVSKLGLAGIRLGYLSAAPALLRE 251

Query: 255 IDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRVERATLIAALRQMPGVEKCWDSEA 314
           +DKVRPPYNV+VL   AALF LEH +V  AQAA +R  R+ L A L  + GV+  + S A
Sbjct: 252 LDKVRPPYNVNVLTEAAALFMLEHLDVLQAQAARLRQARSALAAELAALDGVQ-VFPSAA 310

Query: 315 NMVLIRVADSAKAYEGMKNRKVLVKNVSTMHPLLANCLRLTVGNAEDNAQMLAALQASL 373
           N +LIRV D+ K    +   +VLVKN   MH LL NCLR+TV + ++NA  LAAL+ +L
Sbjct: 311 NFLLIRVPDADKVCASLLAHRVLVKNAGRMHVLLQNCLRITVSSDKENAMFLAALKTAL 369


Lambda     K      H
   0.321    0.134    0.392 

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: 417
Number of extensions: 14
Number of successful extensions: 5
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: 373
Length of database: 372
Length adjustment: 30
Effective length of query: 343
Effective length of database: 342
Effective search space:   117306
Effective search space used:   117306
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate HSERO_RS20335 HSERO_RS20335 (histidinol-phosphate aminotransferase)
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.943.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-96  308.0   0.0    4.4e-96  307.7   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS20335  HSERO_RS20335 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS20335  HSERO_RS20335 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.7   0.0   4.4e-96   4.4e-96       2     347 ..      23     366 ..      22     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 307.7 bits;  conditional E-value: 4.4e-96
                                  TIGR01141   2 ekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealaky 67 
                                                + ++ ++ Y+ +      +++vkL+++EnP+  + +++e+l ++l+  +l+rYp p+ ++lk+a+ k 
  lcl|FitnessBrowser__HerbieS:HSERO_RS20335  23 PVVRGWQSYHVP----SAEGMVKLDAMENPYLLPAELREQLAQRLAalELNRYPVPSYTALKAAICKG 86 
                                                667788888884....55689************************9999******************* PP

                                  TIGR01141  68 lgvee.enillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedle 134
                                                lgv +  ++llgnGsdeli+ll  a+++pg+++l++ep + mY vsak+ag e++ vpl +d + dl+
  lcl|FitnessBrowser__HerbieS:HSERO_RS20335  87 LGVPAgYDVLLGNGSDELITLLSVACAQPGRTILAPEPGFVMYGVSAKMAGLEYVGVPLCADLSLDLP 154
                                                **765279******************************************************999999 PP

                                  TIGR01141 135 avle.aakekvklvflasPnnPtGnllkreeiekvleeve.dalVVvDeAYieFseeasvlellaeyp 200
                                                a+l+  +++k+ +++l +PnnPtG+l + +++ +++e+++  +lVVvDeAY  F+ + + ++ l +++
  lcl|FitnessBrowser__HerbieS:HSERO_RS20335 155 AMLAaMEAHKPVITWLGYPNNPTGTLYEMADVLRIVEAAApYGLVVVDEAYQPFAAS-TLMPALPQHN 221
                                                999868999******************************66***************6.********** PP

                                  TIGR01141 201 nlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkk 268
                                                nlv +rT+SK+  LAg+R+Gy+ a +++ ++l+kvr+pynv++l+ +aa+  l++ d ++++ +++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS20335 222 NLVLMRTVSKLG-LAGIRLGYLSAAPALLRELDKVRPPYNVNVLTEAAALFMLEHLDVLQAQAARLRQ 288
                                                **********86.******************************************************* PP

                                  TIGR01141 269 ererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtr 336
                                                 r  l +el++l+g++v++S aNF+li+v+ da++++ +ll ++++v++ + ++ ll++clRitv ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS20335 289 ARSALAAELAALDGVQVFPSAANFLLIRVP-DADKVCASLLAHRVLVKNAGRMHVLLQNCLRITVSSD 355
                                                ******************************.************************************* PP

                                  TIGR01141 337 eenerllealk 347
                                                +en ++l+alk
  lcl|FitnessBrowser__HerbieS:HSERO_RS20335 356 KENAMFLAALK 366
                                                *********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (372 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: 9.21
//
[ok]

This GapMind analysis is from Apr 09 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