Alignments for a candidate for hisD in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Klebsiella michiganensis M5al

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate BWI76_RS18925 BWI76_RS18925 histidinol dehydrogenase

Query= SwissProt::P10370
         (434 letters)



>FitnessBrowser__Koxy:BWI76_RS18925
          Length = 434

 Score =  738 bits (1906), Expect = 0.0
 Identities = 380/434 (87%), Positives = 406/434 (93%)

Query: 1   MSFNTLIDWNSCSPEQQRALLTRPAISASDSITRTVSDILDNVKTRGDDALREYSAKFDK 60
           MSFNT+IDWN CS EQQ+ LLTRPAISAS SI++TVS+IL NVK  GD ALREYSAKFDK
Sbjct: 1   MSFNTIIDWNGCSAEQQQQLLTRPAISASGSISKTVSEILTNVKDNGDAALREYSAKFDK 60

Query: 61  TEVTALRVTPEEIAAAGARLSDELKQAMTAAVKNIETFHSAQTLPPVDVETQPGVRCQQV 120
           T+V AL+V+ EEIAAAGARLSDELKQAM  AVKNIETFH+AQ L  VDVET PGVRCQQV
Sbjct: 61  TDVKALKVSDEEIAAAGARLSDELKQAMAVAVKNIETFHNAQQLQAVDVETLPGVRCQQV 120

Query: 121 TRPVSSVGLYIPGGSAPLFSTVLMLATPARIAGCQKVVLCSPPPIADEILYAAQLCGVQE 180
           TRP++SVGLYIPGGSAPLFSTVLMLATPARIAGCQ+VVLCSPPPIADEILYAAQLCGV+ 
Sbjct: 121 TRPIASVGLYIPGGSAPLFSTVLMLATPARIAGCQQVVLCSPPPIADEILYAAQLCGVRN 180

Query: 181 IFNVGGAQAIAALAFGSESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVL 240
           IFNVGGAQAIAALAFG+ESV KVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVL
Sbjct: 181 IFNVGGAQAIAALAFGTESVAKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVL 240

Query: 241 VIADSGATPDFVASDLLSQAEHGPDSQVILLTPDADIARKVAEAVERQLAELPRADTARQ 300
           VIADSGATPDFVASDLLSQAEHGPDSQVILLTPD+++A +VA+AVERQLA L RA+TAR 
Sbjct: 241 VIADSGATPDFVASDLLSQAEHGPDSQVILLTPDSEMATRVAQAVERQLAALSRAETARG 300

Query: 301 ALSASRLIVTKDLAQCVAISNQYGPEHLIIQTRNARDLVDAITSAGSVFLGDWSPESAGD 360
           ALSASR+IV +D+AQCVAISNQYGPEHLIIQTRNAR+LVD ITSAGSVFLGDWSPESAGD
Sbjct: 301 ALSASRIIVARDIAQCVAISNQYGPEHLIIQTRNARELVDGITSAGSVFLGDWSPESAGD 360

Query: 361 YASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKAGFSALASTIETLAAAERLTAHK 420
           YASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELS+ GF+ALASTIE LAAAERL AHK
Sbjct: 361 YASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSRDGFAALASTIEILAAAERLDAHK 420

Query: 421 NAVTLRVNALKEQA 434
           NAVTLRV ALKEQA
Sbjct: 421 NAVTLRVAALKEQA 434


Lambda     K      H
   0.315    0.129    0.361 

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: 699
Number of extensions: 19
Number of successful extensions: 1
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: 434
Length of database: 434
Length adjustment: 32
Effective length of query: 402
Effective length of database: 402
Effective search space:   161604
Effective search space used:   161604
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 BWI76_RS18925 BWI76_RS18925 (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.30078.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.9e-163  528.4   2.4   7.9e-163  528.2   2.4    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS18925  BWI76_RS18925 histidinol dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS18925  BWI76_RS18925 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.2   2.4  7.9e-163  7.9e-163       1     393 []      36     426 ..      36     426 .. 0.99

  Alignments for each domain:
  == domain 1  score: 528.2 bits;  conditional E-value: 7.9e-163
                               TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 
                                             v+ei+++v+++Gd+Al+ey+ kfdk+++++l+vs+ee+++a +++++elk+a++ a++nie+fh++q+ + 
  lcl|FitnessBrowser__Koxy:BWI76_RS18925  36 VSEILTNVKDNGDAALREYSAKFDKTDVKALKVSDEEIAAAGARLSDELKQAMAVAVKNIETFHNAQQLQA 106
                                             789******************************************************************** PP

                               TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaa 142
                                             v vet +gv ++q +rp+ +vglY+PgG+a+++Stvlm+a pA++Ag++++v+++Pp     +++++l+aa
  lcl|FitnessBrowser__Koxy:BWI76_RS18925 107 VDVETLPGVRCQQVTRPIASVGLYIPGGSAPLFSTVLMLATPARIAGCQQVVLCSPPP----IADEILYAA 173
                                             *********************************************************6....********* PP

                               TIGR00069 143 kllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvf...gevgidmiaGPsEvlviad 210
                                             +l+gv+++++vGGaqaiaala+Gte+v kvdki+GPGn++Vt+AK++v+   +  +idm+aGPsEvlviad
  lcl|FitnessBrowser__Koxy:BWI76_RS18925 174 QLCGVRNIFNVGGAQAIAALAFGTESVAKVDKIFGPGNAFVTEAKRQVSqrlDGAAIDMPAGPSEVLVIAD 244
                                             *************************************************5444789*************** PP

                               TIGR00069 211 esanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddle 281
                                             + a p++va+DllsqaEH++d+q+il+t+++e+a++v ++ve+ql++l+r+e+a+ +l+  ++ii+++d++
  lcl|FitnessBrowser__Koxy:BWI76_RS18925 245 SGATPDFVASDLLSQAEHGPDSQVILLTPDSEMATRVAQAVERQLAALSRAETARGALS-ASRIIVARDIA 314
                                             ***********************************************************.8********** PP

                               TIGR00069 282 ealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsved 352
                                             +++++sn+y+pEHL++qt++++el++ i++aGsvflG+++pe++gdy++G+nhvLPT+g++ + s+l+++d
  lcl|FitnessBrowser__Koxy:BWI76_RS18925 315 QCVAISNQYGPEHLIIQTRNARELVDGITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLAD 385
                                             *********************************************************************** PP

                               TIGR00069 353 FlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                             F+kr++vqels++++++la+++e la+aE L+aH++av+ R
  lcl|FitnessBrowser__Koxy:BWI76_RS18925 386 FQKRMTVQELSRDGFAALASTIEILAAAERLDAHKNAVTLR 426
                                             **************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (434 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: 11.11
//
[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