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

GapMind for Amino acid biosynthesis

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

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate CA265_RS03635 CA265_RS03635 histidinol dehydrogenase

Query= BRENDA::G7IKX3
         (478 letters)



>FitnessBrowser__Pedo557:CA265_RS03635
          Length = 426

 Score =  400 bits (1028), Expect = e-116
 Identities = 221/430 (51%), Positives = 287/430 (66%), Gaps = 6/430 (1%)

Query: 43  IKTYHLSNLTQTELLSLKSRPRIDFSSVFDIVNPIVDDVHAHGDAAVKQYTSKFDKVDLE 102
           +K Y+ ++L+++++  L SR   D   V + V  I+  V   GD A+  +   FDKVDLE
Sbjct: 1   MKIYNYTDLSKSKIEELCSRQIEDDKLVEERVTDIISTVKKDGDQALFNFAKAFDKVDLE 60

Query: 103 NIVELVSDLPDPVLD-PA-IKEAFDVAYSNIYAFHAAQKSPEKSVENMKGVQCKRVARSI 160
            +     +L     + PA  K+A D AY NI  FH +Q   E  +E M GV C R +R I
Sbjct: 61  KLFLDAEELKSIASNIPAEAKKAIDTAYQNIKTFHQSQLKTEDKIETMPGVMCWRESRPI 120

Query: 161 NSVGLYVPGGTAVLPSTALMLAVPAQIAGCKTIVLANPPTRDGTTCKEVLYCAKKAGVTH 220
             VGLY+PGGTAVLPST LMLA PA IAGCK IV+ +PP  DG T   + YCA   G+  
Sbjct: 121 EKVGLYIPGGTAVLPSTFLMLATPAIIAGCKEIVVCSPPQNDGKTNCYLAYCAVLLGIEK 180

Query: 221 LLKAGGAQAISAMAWGTETCPKVEKIFGPGNQYVTAAKMILQNSEAMVSIDMPAGPSEVL 280
           +   GGAQA++AMA+GTE+ P+V KIFGPGN+YVT AK ++QN    V+IDMPAGPSEVL
Sbjct: 181 VFLIGGAQAVAAMAFGTESVPQVYKIFGPGNRYVTTAKTMVQNK---VAIDMPAGPSEVL 237

Query: 281 VIADKHAIPSHVAADLLSQAEHGPDSQVVLVIAGDGVDQNAIQEEVSKQCQSLPRGEFAA 340
           VIAD+ A PS +AADLL+QAEHG DSQ +LV     +    + +E+  Q   LPR + AA
Sbjct: 238 VIADETANPSFIAADLLAQAEHGTDSQAILVATSYQIIAETL-KEIENQLNVLPRKDIAA 296

Query: 341 KALSHSFIVHARDMLEAITFSNMYAPEHLIINVKDAEKWESFIENAGSVFLGSWTPESVG 400
           KA+++S+ V A+++ EA+ FSN YAPEHLI+  +  +     I NAGSVFLG+ TPES G
Sbjct: 297 KAIANSYAVLAKNLEEAMQFSNEYAPEHLILATEHFQSLIPLITNAGSVFLGNLTPESAG 356

Query: 401 DYASGTNHVLPTYGYARMYSGVSLDSFLKYITVQSLTEEGLRKLGPYVETMAEVEGLEAH 460
           DYASGTNH LPT G+A+ YSGVS D+FLK IT Q L+  GL  +G  VE +A  EGLEAH
Sbjct: 357 DYASGTNHTLPTSGFAKAYSGVSTDAFLKKITFQHLSATGLNNIGRTVEILAAAEGLEAH 416

Query: 461 KRAVTLRLQD 470
           K AV++RL++
Sbjct: 417 KNAVSIRLKN 426


Lambda     K      H
   0.316    0.130    0.378 

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: 488
Number of extensions: 20
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: 478
Length of database: 426
Length adjustment: 33
Effective length of query: 445
Effective length of database: 393
Effective search space:   174885
Effective search space used:   174885
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: 51 (24.3 bits)

Align candidate CA265_RS03635 CA265_RS03635 (histidinol dehydrogenase)
to HMM TIGR00069 (hisD: histidinol dehydrogenase (EC 1.1.1.23))

# 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/TIGR00069.hmm
# target sequence database:        /tmp/gapView.30217.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00069  [M=393]
Accession:   TIGR00069
Description: hisD: histidinol dehydrogenase
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-162  527.6   2.3   1.3e-162  527.4   2.3    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS03635  CA265_RS03635 histidinol dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS03635  CA265_RS03635 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.4   2.3  1.3e-162  1.3e-162       1     393 []      32     423 ..      32     423 .. 1.00

  Alignments for each domain:
  == domain 1  score: 527.4 bits;  conditional E-value: 1.3e-162
                                  TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekql 68 
                                                v++ii+ v+k Gd+Al+++++ fdkv+le+l + +eel++ ++++++e k+a+++a++ni++fh++ql
  lcl|FitnessBrowser__Pedo557:CA265_RS03635  32 VTDIISTVKKDGDQALFNFAKAFDKVDLEKLFLDAEELKSIASNIPAEAKKAIDTAYQNIKTFHQSQL 99 
                                                789***************************************************************** PP

                                  TIGR00069  69 pesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136
                                                +++ ++et++gv++ +  rp+e+vglY+PgG+a +pSt lm+a pA +Ag+keivv++Pp++dgk n 
  lcl|FitnessBrowser__Pedo557:CA265_RS03635 100 KTEDKIETMPGVMCWRESRPIEKVGLYIPGGTAVLPSTFLMLATPAIIAGCKEIVVCSPPQNDGKTNC 167
                                                ******************************************************************** PP

                                  TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsE 204
                                                 + + a llg+++v+ +GGaqa+aa+a+Gte+vp+v ki+GPGn yVt+AK++v+++v+idm+aGPsE
  lcl|FitnessBrowser__Pedo557:CA265_RS03635 168 YLAYCAVLLGIEKVFLIGGAQAVAAMAFGTESVPQVYKIFGPGNRYVTTAKTMVQNKVAIDMPAGPSE 235
                                                ******************************************************************** PP

                                  TIGR00069 205 vlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekng 272
                                                vlviade+anp+++aaDll+qaEH++d+qailv+ts ++++++ +e+e+ql+ l+rk+ia k+++ n+
  lcl|FitnessBrowser__Pedo557:CA265_RS03635 236 VLVIADETANPSFIAADLLAQAEHGTDSQAILVATSYQIIAETLKEIENQLNVLPRKDIAAKAIA-NS 302
                                                *****************************************************************.89 PP

                                  TIGR00069 273 aiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsg 340
                                                + +l+++leea+++sneyApEHL+l+t++ ++l++ i+naGsvflG+ tpe++gdy++G+nh+LPTsg
  lcl|FitnessBrowser__Pedo557:CA265_RS03635 303 YAVLAKNLEEAMQFSNEYAPEHLILATEHFQSLIPLITNAGSVFLGNLTPESAGDYASGTNHTLPTSG 370
                                                9999**************************************************************** PP

                                  TIGR00069 341 tArfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                                +A+++sg+s++ Flk+i++q+ls ++l++++++ve la+aEgLeaH++av++R
  lcl|FitnessBrowser__Pedo557:CA265_RS03635 371 FAKAYSGVSTDAFLKKITFQHLSATGLNNIGRTVEILAAAEGLEAHKNAVSIR 423
                                                ***************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (426 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: 11.22
//
[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