Alignments for a candidate for hisD in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Phaeobacter inhibens BS107

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (uncharacterized)
to candidate GFF761 PGA1_c07750 histidinol dehydrogenase HisD

Query= curated2:Q465R4
         (433 letters)



>FitnessBrowser__Phaeo:GFF761
          Length = 435

 Score =  267 bits (683), Expect = 4e-76
 Identities = 152/412 (36%), Positives = 238/412 (57%), Gaps = 9/412 (2%)

Query: 21  LSRGSGLEDVAKTVSTVLSDVRTKGDSALREYTAKFDKVELANFGVSEEEFQQALSGISP 80
           L+  S   +  KTV  +L D+   GD+   EY AKFD+ E  N  +++EE + A + +  
Sbjct: 11  LTPKSDASETHKTVQGILDDIEAGGDAKALEYAAKFDRYE-GNVLLTDEEIEAACALVPE 69

Query: 81  ELLDHLKSAAANIRAFHEAQLPKATWF---MELKPGIVLGQKATPLESVGAYAPGGRASY 137
           +L   ++ +  N+R F  A+L K+T      E+ PG + GQK  P+++ G Y PGGR S+
Sbjct: 70  KLKADIRFSHDNVRRF--AELQKSTMQNVETEICPGFITGQKVIPVDAAGCYVPGGRYSH 127

Query: 138 PSTVLMTVIPARVAGVEQVIVCTPPRPDGSVHPLTLAAAKVAGADKVFKLGGVQAIGSMA 197
            ++ +MTV  A+VAG + +  C+PPRP   V P  + AA + GADK+  +GGVQ + +M 
Sbjct: 128 IASAIMTVTTAKVAGCKHITACSPPRPGVGVAPAIVYAAHICGADKIMAMGGVQGVAAMT 187

Query: 198 YGTETVPKVDKIVGPGNVFVTAAKMQIRDVAEIDFPAGPSEVLIIADESADAVMVASDIL 257
           +G   +PK + +VGPGN FV  AK  +     ID  AGP++ LI+AD +ADA +VA+D++
Sbjct: 188 FGLFGLPKANILVGPGNQFVAEAKRILFGRVGIDMIAGPTDSLILADRTADAHIVATDLV 247

Query: 258 AQSEHDPNSVSILVTGSDTLAEAVKREV---LVQAEQAARSSIIKSSLENAAILIADSLE 314
           +Q+EH  NS   LVT    LAE V R V   +    +  R +   +  + A +++    E
Sbjct: 248 SQAEHGYNSPVWLVTDDRALAEEVMRLVPGLIDDLPEVNRENAAAAWRDYAEVILCSDRE 307

Query: 315 QCIGFSNKFAPEHLEIMVADPDFVLDRIKNAGSIFIGNYSPVPVGDYASGTNHVLPTSGY 374
           +    S+ +APEHL +   D D+ L ++   GS+F+G  + V  GD A+GTNHVLPTS  
Sbjct: 308 EMAACSDDYAPEHLTVQAEDLDWWLGQLTCYGSLFLGEETTVSYGDKAAGTNHVLPTSRA 367

Query: 375 ARVYSGLNINHFIKYSSIQRISKSGLESLKETVIALAEEEGLQAHADAIRTR 426
           A    GL+++ ++K  + QR ++ G +++ E    +A  EG++ HA A   R
Sbjct: 368 ASYTGGLSVHKYMKIVTWQRATREGSKAVAEATARIARLEGMEGHARAADVR 419


Lambda     K      H
   0.315    0.131    0.360 

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: 400
Number of extensions: 19
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: 433
Length of database: 435
Length adjustment: 32
Effective length of query: 401
Effective length of database: 403
Effective search space:   161603
Effective search space used:   161603
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: 51 (24.3 bits)

Align candidate GFF761 PGA1_c07750 (histidinol dehydrogenase HisD)
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.20863.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.1e-137  444.5   0.1   2.3e-137  444.3   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF761  PGA1_c07750 histidinol dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF761  PGA1_c07750 histidinol dehydrogenase HisD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.3   0.1  2.3e-137  2.3e-137       1     393 []      24     419 ..      24     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 444.3 bits;  conditional E-value: 2.3e-137
                         TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes..veve 75 
                                       v+ i++d+++ Gd+  ley+ kfd+++  ++ +++ee+e+a + v+e+lk++++ +++n+++f+e q+++   ve+e
  lcl|FitnessBrowser__Phaeo:GFF761  24 VQGILDDIEAGGDAKALEYAAKFDRYE-GNVLLTDEEIEAACALVPEKLKADIRFSHDNVRRFAELQKSTMqnVETE 99 
                                       789***********************6.899**********************************998654349999 PP

                         TIGR00069  76 teegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdevyk 152
                                       + +g ++gqkv p++++g+YvPgG+++++++++mt+ +AkvAg+k+i++++Pp+    v+pa+++aa+++g+d++++
  lcl|FitnessBrowser__Phaeo:GFF761 100 ICPGFITGQKVIPVDAAGCYVPGGRYSHIASAIMTVTTAKVAGCKHITACSPPRPGVGVAPAIVYAAHICGADKIMA 176
                                       99***************************************************98888******************* PP

                         TIGR00069 153 vGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqaEHd 229
                                       +GG+q++aa+++G+  +pk++++vGPGn++V++AK+++fg+vgidmiaGP++ l++ad++a++++va+Dl+sqaEH+
  lcl|FitnessBrowser__Phaeo:GFF761 177 MGGVQGVAAMTFGLFGLPKANILVGPGNQFVAEAKRILFGRVGIDMIAGPTDSLILADRTADAHIVATDLVSQAEHG 253
                                       ***************************************************************************** PP

                         TIGR00069 230 edaqailvttseelaekveeeveeqleele..rkeiaekslekngaiilvddleealelsneyApEHLelqtkdpee 304
                                        ++ ++lvt++++lae+v + v   +++l+  ++e a +++++++++il++d ee++++s++yApEHL++q++d   
  lcl|FitnessBrowser__Phaeo:GFF761 254 YNSPVWLVTDDRALAEEVMRLVPGLIDDLPevNRENAAAAWRDYAEVILCSDREEMAACSDDYAPEHLTVQAEDLDW 330
                                       *****************************9667999***************************************** PP

                         TIGR00069 305 llkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaE 381
                                       +l +++ +Gs+flGe t++++gd++aG+nhvLPTs++A +++glsv++++k +++q++++e+ +++aea++++a++E
  lcl|FitnessBrowser__Phaeo:GFF761 331 WLGQLTCYGSLFLGEETTVSYGDKAAGTNHVLPTSRAASYTGGLSVHKYMKIVTWQRATREGSKAVAEATARIARLE 407
                                       ***************************************************************************** PP

                         TIGR00069 382 gLeaHaeavevR 393
                                       g+e Ha+a++vR
  lcl|FitnessBrowser__Phaeo:GFF761 408 GMEGHARAADVR 419
                                       ********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (435 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: 12.24
//
[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