Alignments for a candidate for hisN in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisN in Pedobacter sp. GW460-11-11-14-LB5

Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate CA265_RS03625 CA265_RS03625 bifunctional imidazole glycerol-phosphate dehydratase/histidinol phosphatase

Query= SwissProt::D2QPE6
         (382 letters)



>FitnessBrowser__Pedo557:CA265_RS03625
          Length = 377

 Score =  480 bits (1236), Expect = e-140
 Identities = 237/382 (62%), Positives = 285/382 (74%), Gaps = 5/382 (1%)

Query: 1   MQKIVFIDRDGTLIAEPQPDQQVDSLAKLDFIPKAISAMRKIAEDTTYELVMVTNQDGLG 60
           M+K++FIDRDGTL  EP  D+QVDS AKL F P+++  + KIA +  YELVMVTNQDGLG
Sbjct: 1   MKKVLFIDRDGTLNIEPD-DEQVDSFAKLKFYPRSLYYLSKIAAELDYELVMVTNQDGLG 59

Query: 61  TGSFPEDTFWPAHNKMMSTFAGENVNFAAVHIDRHFPHDNSSTRKPGVGMLTQYFEASYD 120
           T S PE+ FWP HN M+ TF GE V+F+ + IDR F  DN+ TRKPG  +LT+YF   YD
Sbjct: 60  TLSNPEENFWPIHNFMLDTFEGEGVHFSEIVIDRTFAKDNAPTRKPGTALLTKYFSEDYD 119

Query: 121 LTNSFVIGDRLTDVQLAVNLGAKAILFMPPNGLAAVQSADVSGLTEAMKQAIVLQTGDWD 180
           L NSFVIGDRL DV LA NLGAKAI     + L + ++ D     E +   I+L+T  W+
Sbjct: 120 LKNSFVIGDRLNDVVLAKNLGAKAIFLRQNDALGSTEALDKH---ETLLDVIILETKKWE 176

Query: 181 EIYEFLRLPARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADL 240
           +IY  L+  +R    ER T ET I + L+LDG G+A + TGL FFDHMLDQ+A+H   DL
Sbjct: 177 DIYNLLKAGSRKIHHERKTNETDITINLDLDGTGKAKIETGLNFFDHMLDQIARHGSVDL 236

Query: 241 AIHVNGDLHIDEHHTIEDTALALGEAYRRALGDKRGISRYGFLLPMDEALAQVGIDFSGR 300
            +   GDLHIDEHHTIEDT +ALGEA+ + LG+K GI RYGF LPMD+ LAQV IDF GR
Sbjct: 237 EVIAKGDLHIDEHHTIEDTGIALGEAFAKGLGNKLGIERYGFCLPMDDCLAQVAIDFGGR 296

Query: 301 PWLVWDAEFKREKIGDMPTEMFYHFFKSFSDTALCNLNIKVEGDNEHHKIEAIFKAFAKA 360
            W+VWDAEFKREK+GDMPTEMFYHFFKSFSD A CNLN+K EGDNEHHKIEAIFKAFAKA
Sbjct: 297 NWIVWDAEFKREKVGDMPTEMFYHFFKSFSDAAKCNLNVKAEGDNEHHKIEAIFKAFAKA 356

Query: 361 IKMAVRRDINELDNLPSTKGVL 382
           IKMA++RD  ++  LPSTKG+L
Sbjct: 357 IKMAIKRDAEKM-VLPSTKGLL 377


Lambda     K      H
   0.320    0.136    0.403 

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: 451
Number of extensions: 14
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: 382
Length of database: 377
Length adjustment: 30
Effective length of query: 352
Effective length of database: 347
Effective search space:   122144
Effective search space used:   122144
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: 50 (23.9 bits)

Align candidate CA265_RS03625 CA265_RS03625 (bifunctional imidazole glycerol-phosphate dehydratase/histidinol phosphatase)
to HMM TIGR01261 (hisB: histidinol-phosphatase (EC 3.1.3.15))

# 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/TIGR01261.hmm
# target sequence database:        /tmp/gapView.16987.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01261  [M=161]
Accession:   TIGR01261
Description: hisB_Nterm: histidinol-phosphatase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    2.9e-50  156.0   0.0    4.7e-50  155.3   0.0    1.3  1  lcl|FitnessBrowser__Pedo557:CA265_RS03625  CA265_RS03625 bifunctional imida


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS03625  CA265_RS03625 bifunctional imidazole glycerol-phosphate dehydratase/histid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3   0.0   4.7e-50   4.7e-50       1     149 [.       2     149 ..       2     158 .. 0.96

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 4.7e-50
                                  TIGR01261   1 qkilfidrdGtlieePksdfqvdaleklklekkvipallklk.eagyklvlvtnqdGlGtesfPkedf 67 
                                                +k+lfidrdGtl  eP  d qvd++ klk+ +  +  l k+  e++y+lv+vtnqdGlGt s P+e+f
  lcl|FitnessBrowser__Pedo557:CA265_RS03625   2 KKVLFIDRDGTLNIEPD-DEQVDSFAKLKFYPRSLYYLSKIAaELDYELVMVTNQDGLGTLSNPEENF 68 
                                                589*************9.99********************96379*********************** PP

                                  TIGR01261  68 dkphalmlqifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlql 135
                                                   h++ml+ f+ eG++f++++i++ f +dn+ +rkP ++ll++y+ +e++d ++s+viGdr  d+ l
  lcl|FitnessBrowser__Pedo557:CA265_RS03625  69 WPIHNFMLDTFEGEGVHFSEIVIDRTFAKDNAPTRKPGTALLTKYF-SEDYDLKNSFVIGDRLNDVVL 135
                                                **********************************************.789****************** PP

                                  TIGR01261 136 aenlgirglkykee 149
                                                a+nlg +++ ++++
  lcl|FitnessBrowser__Pedo557:CA265_RS03625 136 AKNLGAKAIFLRQN 149
                                                ********988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (161 nodes)
Target sequences:                          1  (377 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.64
//
[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