Alignments for a candidate for hisC in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Cupriavidus basilensis 4G11

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate RR42_RS04465 RR42_RS04465 aspartate aminotransferase

Query= metacyc::BSU22620-MONOMER
         (360 letters)



>FitnessBrowser__Cup4G11:RR42_RS04465
          Length = 371

 Score =  250 bits (639), Expect = 4e-71
 Identities = 151/361 (41%), Positives = 202/361 (55%), Gaps = 6/361 (1%)

Query: 5   EHLKQLKPYQPGKPIEAVKSEYGL--DKVVKLASNENPYGCSEAAKEALHHEIQQLALYP 62
           E+++ + PY  GKPI  V  E+GL    +VKLASNENP G  E+A+ A+   +  L  YP
Sbjct: 11  EYVRAISPYVAGKPISEVAREFGLVESTIVKLASNENPLGMPESARTAIAAAVADLGRYP 70

Query: 63  DGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNA 122
           D    AL+  LS   +V    L  GNGS++I++I   A +    + V A  +F  Y    
Sbjct: 71  DANGFALKGALSARFDVPPDWLTLGNGSNDILEIAAHALVKPGESIVYAEHSFAVYALAT 130

Query: 123 VIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVP 182
              GA   E+  R D  HDLDAM  AI   T++V+I +PNNPTGT+    E+  FL +VP
Sbjct: 131 QEVGARAIEVKAR-DYGHDLDAMAVAIAPDTRLVFIANPNNPTGTFLPAAEIETFLAKVP 189

Query: 183 SRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLI 242
           + V+VVLDEAY EY+      +++  + KY NL++ RTFSKAYGLA LR+GY +A   L 
Sbjct: 190 ADVVVVLDEAYNEYLDDAQQYDSIAWVRKYPNLLVSRTFSKAYGLAGLRIGYAVAQPALT 249

Query: 243 RQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQT 302
             +   R+PFN + L QAAA+AAL D AF+    E N AG  Q        GL+  PS  
Sbjct: 250 DLLNRIRQPFNVNSLAQAAAVAALGDAAFLQRSAELNRAGKAQLVAAFDRLGLQYVPSSG 309

Query: 303 NFVLIDFKR---PADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEI 359
           NFVL+   R       +  ALL++G IVR       P  LRITIG  E+N   +A L + 
Sbjct: 310 NFVLVRVGRDDGAGARVNLALLKQGVIVRPVGNYNLPQWLRITIGLPEENAAFIAALEKA 369

Query: 360 L 360
           L
Sbjct: 370 L 370


Lambda     K      H
   0.317    0.134    0.382 

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: 301
Number of extensions: 14
Number of successful extensions: 4
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: 360
Length of database: 371
Length adjustment: 30
Effective length of query: 330
Effective length of database: 341
Effective search space:   112530
Effective search space used:   112530
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 RR42_RS04465 RR42_RS04465 (aspartate 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.3695.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-111  356.8   0.0   5.9e-111  356.7   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS04465  RR42_RS04465 aspartate aminotran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS04465  RR42_RS04465 aspartate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.7   0.0  5.9e-111  5.9e-111       3     348 ..      12     368 ..      10     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 356.7 bits;  conditional E-value: 5.9e-111
                                 TIGR01141   3 kikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkea 63 
                                                +++++pY++g      are+g     +vkL+snEnP+g++e+++ a+ +++++l rYpd+++++lk a
  lcl|FitnessBrowser__Cup4G11:RR42_RS04465  12 YVRAISPYVAGkpisevAREFGLVesTIVKLASNENPLGMPESARTAIAAAVADLGRYPDANGFALKGA 80 
                                               5899*************9999998889****************************************** PP

                                 TIGR01141  64 lakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqed 132
                                               l+++++v ++ ++lgnGs++++e+ ++a+++pg++++++e+++++Y++ ++  ga+ +ev++++ g +d
  lcl|FitnessBrowser__Cup4G11:RR42_RS04465  81 LSARFDVPPDWLTLGNGSNDILEIAAHALVKPGESIVYAEHSFAVYALATQEVGARAIEVKARDYG-HD 148
                                               ****************************************************************95.9* PP

                                 TIGR01141 133 leavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlella 197
                                               l+a+++a++ +++lvf+a+PnnPtG++l ++eie++l++v +d++VV+DeAY+e+ ++   ++ + +++
  lcl|FitnessBrowser__Cup4G11:RR42_RS04465 149 LDAMAVAIAPDTRLVFIANPNNPTGTFLPAAEIETFLAKVpADVVVVLDEAYNEYLDDaqqYDSIAWVR 217
                                               ****************************************88*************9998889999**** PP

                                 TIGR01141 198 eypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveev 266
                                               +ypnl+v+rT+SKa+gLAglR+Gya+a++++ + l+++r+p+nv+sla++aavaal d+++++++ e +
  lcl|FitnessBrowser__Cup4G11:RR42_RS04465 218 KYPNLLVSRTFSKAYGLAGLRIGYAVAQPALTDLLNRIRQPFNVNSLAQAAAVAALGDAAFLQRSAELN 286
                                               ********************************************************************* PP

                                 TIGR01141 267 kkererlleelkkleglevyeSkaNFvlikvke...daeelleallekgiivRdlksaeglleeclRit 332
                                               ++++++l +++  l gl++++S +NFvl++v +   + +++  all++g+ivR ++++ + l+++lRit
  lcl|FitnessBrowser__Cup4G11:RR42_RS04465 287 RAGKAQLVAAFDRL-GLQYVPSSGNFVLVRVGRddgAGARVNLALLKQGVIVRPVGNY-N-LPQWLRIT 352
                                               **************.8***************998888899999***************.5.6******* PP

                                 TIGR01141 333 vGtreenerllealke 348
                                               +G +een ++++al++
  lcl|FitnessBrowser__Cup4G11:RR42_RS04465 353 IGLPEENAAFIAALEK 368
                                               *************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (371 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: 10.01
//
[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