Alignments for a candidate for hisC in Trichodesmium erythraeum IMS101

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Trichodesmium erythraeum IMS101

Align Histidinol-phosphate aminotransferase 2; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 2 (uncharacterized)
to candidate WP_011613971.1 TERY_RS22660 histidinol-phosphate aminotransferase

Query= curated2:Q3MAX6
         (380 letters)



>NCBI__GCF_000014265.1:WP_011613971.1
          Length = 376

 Score =  438 bits (1126), Expect = e-127
 Identities = 233/379 (61%), Positives = 278/379 (73%), Gaps = 11/379 (2%)

Query: 1   MLPFIRSDLAQFTAYKPHPSSDTDAAVPAQLDRLDTNESPCDLPPELKQKLAWTFQQVIE 60
           M  FIRS+L    AY PH +  ++      LDRLDTNE P DLP  LKQKLA  +QQ+IE
Sbjct: 1   MFTFIRSNLNNLKAYTPHSAGSSEIL----LDRLDTNECPYDLPDNLKQKLAENYQQLIE 56

Query: 61  SNRYPDGGHEELKDAIAQYVNESANISSSPITAANISVGNGSDELIRSLLIATCLGAQGS 120
           +NRYPDG H +LK+AIA+YVNE     S+ I+A NISVGNGSDELIRSLLI TC+G +GS
Sbjct: 57  TNRYPDGSHLKLKEAIAKYVNEVT--PSANISANNISVGNGSDELIRSLLIVTCVGGEGS 114

Query: 121 ILVANPTFSMYGILAQTLGIPVVTVSRNPENFEIDLTAAQSAIEQTQNPPIRVVFVVHPN 180
           IL A PTFSMY ILAQTLGIPVV V R   NFEID+TAA+ AI  T+NP I+ +FVVHPN
Sbjct: 115 ILTATPTFSMYSILAQTLGIPVVNVGRKESNFEIDITAAEDAINHTKNPSIKAIFVVHPN 174

Query: 181 SPTANPLTTNELRWLKSLSEQILVVVDEAYFEFSQTTLISELVQRPNWVILRTFSKAFRL 240
           SPTAN L + EL WL+SL + ILVV+DEAYFEFSQT+L  EL Q PNWVILRTFSKAFRL
Sbjct: 175 SPTANALNSQELVWLRSLPDDILVVIDEAYFEFSQTSLAEELNQHPNWVILRTFSKAFRL 234

Query: 241 AAMRVGYCVAHPEAIAILEKVRLPYNLPSFSITSALVALQNRAILLESIPQILNERAKLI 300
           A++RVGY +AHPE I  LEKVRLPYNLPSFS  +A + L +   LL  IP+IL ER+KL 
Sbjct: 235 ASLRVGYAIAHPEIIINLEKVRLPYNLPSFSQAAAQLVLNHSQHLLSFIPEILRERSKLF 294

Query: 301 TALSKYPELAVAESAANFIFLQ-----LKTDNKNSPDTALLNLHQQLKNSGTLVRQISGG 355
               + P L V +SAANF++++     LK   K+S D +L +L Q+LK  GTL+R   GG
Sbjct: 295 ATFGEIPALKVWKSAANFLYMRLTDEGLKLMGKSSQDQSLSSLMQRLKTQGTLIRHTGGG 354

Query: 356 LRITIGTPEENIRTLNHIQ 374
           LRITIGT EEN RT+  I+
Sbjct: 355 LRITIGTSEENQRTVERIK 373


Lambda     K      H
   0.317    0.131    0.371 

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: 453
Number of extensions: 18
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: 380
Length of database: 376
Length adjustment: 30
Effective length of query: 350
Effective length of database: 346
Effective search space:   121100
Effective search space used:   121100
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: 50 (23.9 bits)

Align candidate WP_011613971.1 TERY_RS22660 (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.17423.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.2e-88  283.3   0.0    1.4e-88  283.0   0.0    1.0  1  lcl|NCBI__GCF_000014265.1:WP_011613971.1  TERY_RS22660 histidinol-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000014265.1:WP_011613971.1  TERY_RS22660 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.0   0.0   1.4e-88   1.4e-88       1     347 [.       6     373 ..       6     375 .. 0.92

  Alignments for each domain:
  == domain 1  score: 283.0 bits;  conditional E-value: 1.4e-88
                                 TIGR01141   1 rekikklepYqpgarelgekevv..kLnsnEnPfgpsekvkealkeelk...klhrYpdpqalelkeal 64 
                                               r ++++l++Y+p  ++ g +e++  +L++nE P++ ++++k++l e+ +   + +rYpd ++l+lkea+
  lcl|NCBI__GCF_000014265.1:WP_011613971.1   6 RSNLNNLKAYTP--HSAGSSEILldRLDTNECPYDLPDNLKQKLAENYQqliETNRYPDGSHLKLKEAI 72 
                                               678999999999..456665544448*******************998878899*************** PP

                                 TIGR01141  65 akylg.......veeenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevpl 125
                                               aky++       ++++ni +gnGsdeli+ l+  ++  g  ++l++ pt+smY++ a++ g+ v++v  
  lcl|NCBI__GCF_000014265.1:WP_011613971.1  73 AKYVNevtpsanISANNISVGNGSDELIRSLLIVTCVGGeGSILTATPTFSMYSILAQTLGIPVVNVGR 141
                                               *****************************999999999979**************************** PP

                                 TIGR01141 126 ked.....gqedleavleaakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFsee 189
                                               ke+      +   +a++++++ ++k +f+ +Pn Pt n l+++e++ +     d lVV+DeAY eFs++
  lcl|NCBI__GCF_000014265.1:WP_011613971.1 142 KESnfeidITAAEDAINHTKNPSIKAIFVVHPNSPTANALNSQELVWLRSLPDDILVVIDEAYFEFSQT 210
                                               999754433344555556888899**********************9999989***************6 PP

                                 TIGR01141 190 asvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdk 258
                                                s +e l+++pn v+lrT+SKaf LA+lRvGyaia++eii  lekvr pyn++s +++aa   l++s++
  lcl|NCBI__GCF_000014265.1:WP_011613971.1 211 -SLAEELNQHPNWVILRTFSKAFRLASLRVGYAIAHPEIIINLEKVRLPYNLPSFSQAAAQLVLNHSQH 278
                                               .******************************************************************** PP

                                 TIGR01141 259 iektveevkkererlleelkkleglevyeSkaNFvlikvke.............daeelleallekgii 314
                                               + + + e+ +er  l++ + +++ l+v +S aNF+ +++                 + l+++l+ +g +
  lcl|NCBI__GCF_000014265.1:WP_011613971.1 279 LLSFIPEILRERSKLFATFGEIPALKVWKSAANFLYMRLTDeglklmgkssqdqSLSSLMQRLKTQGTL 347
                                               **************************************9988999999998766667899********* PP

                                 TIGR01141 315 vRdlksaeglleeclRitvGtreenerllealk 347
                                               +R+ +   g     lRit+Gt+een+r +e +k
  lcl|NCBI__GCF_000014265.1:WP_011613971.1 348 IRHTG---G----GLRITIGTSEENQRTVERIK 373
                                               **998...3....48*************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (376 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: 00:00:00.02
# Mc/sec: 6.53
//
[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