GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Desulforamulus ruminis DSM 2154

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_013841335.1 DESRU_RS06590 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000215085.1:WP_013841335.1
          Length = 432

 Score =  394 bits (1011), Expect = e-114
 Identities = 206/412 (50%), Positives = 275/412 (66%), Gaps = 1/412 (0%)

Query: 18  AFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAF 77
           A L G+    E +   V  I+  VR  GD AL  ++RRFD   L    + VT+ EID A+
Sbjct: 15  ALLKGRSGGQEGIASRVAAIMQEVRERGDIALCGFTRRFDGASLTPEQLRVTDEEIDQAY 74

Query: 78  DAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTAS 137
                  + +LKLARDRI K+H +QL +    T+  G  LG   T ++ VG+YVPGGTAS
Sbjct: 75  SMVDQEVLTSLKLARDRIRKYHQKQLTRSWFDTEPNGTLLGQLITPLDRVGVYVPGGTAS 134

Query: 138 YPSSVLMNAMPAKVAGVDRIVMVVP-APDGNLNPLVLVAARLAGVSEIYRVGGAQAIAAL 196
           YPSSVLMNA+PAKVAGV ++VMV P   DG LNP  LVAAR AGV EIY+ GGAQAIAAL
Sbjct: 135 YPSSVLMNAVPAKVAGVSQVVMVTPPGADGKLNPYTLVAAREAGVDEIYKAGGAQAIAAL 194

Query: 197 AYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADL 256
           AYGTETI PV KI GPGN +V  AKR+V+G V IDM+AGPSEVL+VAD   NP++ AAD+
Sbjct: 195 AYGTETIAPVDKITGPGNIFVTLAKRMVYGQVDIDMLAGPSEVLVVADASANPEYAAADM 254

Query: 257 LAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFED 316
           L+QAEHD  A ++L+T+    A  V + +E+Q+  L R + A  +  +  A+++    E+
Sbjct: 255 LSQAEHDVLASAVLLTHHRELAEWVRQELEKQVALLPRQDLAREALANHSALVITGSLEE 314

Query: 317 AIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSA 376
           ++ LAN  A EHLE+ V +   ++ RIR+AG++F+G ++PE +GDY+ G NHVLPT  +A
Sbjct: 315 SLELANAFAPEHLELLVEEPFRWLSRIRHAGAVFLGAHSPEPVGDYLAGPNHVLPTGGTA 374

Query: 377 RFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRL 428
           RF S L+V  +MK++S++    E L  LGP  I +A  EGL AHA +V +RL
Sbjct: 375 RFYSPLNVDTFMKKSSIISFSKENLELLGPDIIRLAEVEGLQAHANAVRVRL 426


Lambda     K      H
   0.318    0.134    0.375 

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: 462
Number of extensions: 14
Number of successful extensions: 2
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: 430
Length of database: 432
Length adjustment: 32
Effective length of query: 398
Effective length of database: 400
Effective search space:   159200
Effective search space used:   159200
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 WP_013841335.1 DESRU_RS06590 (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.3887205.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-174  565.0   0.0   6.1e-174  564.8   0.0    1.0  1  NCBI__GCF_000215085.1:WP_013841335.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013841335.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  564.8   0.0  6.1e-174  6.1e-174       1     393 []      31     425 ..      31     425 .. 0.99

  Alignments for each domain:
  == domain 1  score: 564.8 bits;  conditional E-value: 6.1e-174
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 
                                           v++i+++vr++Gd Al  +t++fd++  ++e+lrv++ee+++a++ vd+e+ ++l+la ++i+k+h+kql++s
  NCBI__GCF_000215085.1:WP_013841335.1  31 VAAIMQEVRERGDIALCGFTRRFDGAslTPEQLRVTDEEIDQAYSMVDQEVLTSLKLARDRIRKYHQKQLTRS 103
                                           789**********************977899****************************************** PP

                             TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144
                                           ++ ++ +g+llgq+++pl+rvg+YvPgG+a+ypS+vlm+avpAkvAgv+++v+vtPp  dgk+np +l+aa+ 
  NCBI__GCF_000215085.1:WP_013841335.1 104 WFDTEPNGTLLGQLITPLDRVGVYVPGGTASYPSSVLMNAVPAKVAGVSQVVMVTPPGADGKLNPYTLVAARE 176
                                           ************************************************************************* PP

                             TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217
                                           +gvde+yk+GGaqaiaalayGtet+ +vdki+GPGni+Vt AK++v+g+v+idm+aGPsEvlv+ad+sanpe+
  NCBI__GCF_000215085.1:WP_013841335.1 177 AGVDEIYKAGGAQAIAALAYGTETIAPVDKITGPGNIFVTLAKRMVYGQVDIDMLAGPSEVLVVADASANPEY 249
                                           ************************************************************************* PP

                             TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsney 290
                                            aaD+lsqaEHd  a+a+l+t+++elae v++e+e+q++ l+r+++a+++l++++a++++ +lee lel+n++
  NCBI__GCF_000215085.1:WP_013841335.1 250 AAADMLSQAEHDVLASAVLLTHHRELAEWVRQELEKQVALLPRQDLAREALANHSALVITGSLEESLELANAF 322
                                           ************************************************************************* PP

                             TIGR00069 291 ApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqels 363
                                           ApEHLel +++p ++l++i++aG+vflG+++pe++gdy+aGpnhvLPT+gtArf+s+l+v++F+k++s++++s
  NCBI__GCF_000215085.1:WP_013841335.1 323 APEHLELLVEEPFRWLSRIRHAGAVFLGAHSPEPVGDYLAGPNHVLPTGGTARFYSPLNVDTFMKKSSIISFS 395
                                           ************************************************************************* PP

                             TIGR00069 364 kealeelaeaveklaeaEgLeaHaeavevR 393
                                           ke+le l++++++lae+EgL+aHa+av+vR
  NCBI__GCF_000215085.1:WP_013841335.1 396 KENLELLGPDIIRLAEVEGLQAHANAVRVR 425
                                           ****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (432 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: 00:00:00.00
# Mc/sec: 17.53
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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