GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Azorhizobium caulinodans ORS 571

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_012172788.1 AZC_RS21905 histidinol-phosphatase

Query= reanno::Phaeo:GFF2154
         (250 letters)



>NCBI__GCF_000010525.1:WP_012172788.1
          Length = 262

 Score =  227 bits (579), Expect = 2e-64
 Identities = 120/245 (48%), Positives = 154/245 (62%), Gaps = 2/245 (0%)

Query: 1   MADAARQAILPYFRSA-GLQSDNKLD-EGFDPVTIADRAAEQAMRSVLSELRPEDSILGE 58
           +A  + +AILP+FR+A G++   +   + FDPVT ADRAAEQ MR +++   PE  I+GE
Sbjct: 13  LATRSGEAILPFFRTAIGVEDKGRRKGQSFDPVTEADRAAEQVMRRMITTTFPEHGIIGE 72

Query: 59  EFGETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGT 118
           EFG     +   W LDPIDGT+ FISG P WG LI L     P  G++ QP+IGERF G 
Sbjct: 73  EFGNERRDADYVWALDPIDGTKSFISGMPAWGTLIGLLKQGAPVYGMMHQPFIGERFFGD 132

Query: 119 PEGASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDC 178
              A   GP G   L+TR    L +A LFTT P +   A+R  FQ V   VRL+RYG DC
Sbjct: 133 GGSAHYLGPAGKRRLLTRDCGRLEDAILFTTSPLLMNAADRTLFQSVERDVRLSRYGGDC 192

Query: 179 YAYALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAEL 238
           YAY ++AAG  DLVIE GL  +DI A + VI+ AGG+VTNW+G     GG+V+AA +  +
Sbjct: 193 YAYCMVAAGLVDLVIETGLQDHDIVALVPVIEGAGGIVTNWEGGSPVAGGRVVAAGSKAV 252

Query: 239 HAAAL 243
           H  AL
Sbjct: 253 HEQAL 257


Lambda     K      H
   0.317    0.134    0.392 

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: 219
Number of extensions: 12
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: 250
Length of database: 262
Length adjustment: 24
Effective length of query: 226
Effective length of database: 238
Effective search space:    53788
Effective search space used:    53788
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: 47 (22.7 bits)

Align candidate WP_012172788.1 AZC_RS21905 (histidinol-phosphatase)
to HMM TIGR02067 (hisN: 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/TIGR02067.hmm
# target sequence database:        /tmp/gapView.667959.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02067  [M=252]
Accession:   TIGR02067
Description: his_9_HisN: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-99  318.7   0.0    1.6e-99  318.5   0.0    1.0  1  NCBI__GCF_000010525.1:WP_012172788.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_012172788.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.5   0.0   1.6e-99   1.6e-99       2     252 .]       7     261 ..       6     261 .. 0.98

  Alignments for each domain:
  == domain 1  score: 318.5 bits;  conditional E-value: 1.6e-99
                             TIGR02067   2 lalalelaeaageailkyfrasdlkvdkksdk....tpVteADraaEeaireliaakfPddgilGEEfgeeee 70 
                                           +a++++la+ +geail++fr+   ++dk ++k    +pVteADraaE+++r++i+++fP++gi+GEEfg+e+ 
  NCBI__GCF_000010525.1:WP_012172788.1   7 DAFVHDLATRSGEAILPFFRTAIGVEDKGRRKgqsfDPVTEADRAAEQVMRRMITTTFPEHGIIGEEFGNERR 79 
                                           5899*****************99999999998999************************************** PP

                             TIGR02067  71 daeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallng.gerelrvsev 142
                                           da+yvW lDPiDGTksFi+G+P wgtLi+Ll++g+pv G+++qP++gerf+++ g++ +l + g+r+l ++ +
  NCBI__GCF_000010525.1:WP_012172788.1  80 DADYVWALDPIDGTKSFISGMPAWGTLIGLLKQGAPVYGMMHQPFIGERFFGDGGSAHYLGPaGKRRLLTRDC 152
                                           ************************************************************98667******** PP

                             TIGR02067 143 aklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipiie 215
                                            +l+dA+l+ttsp  l++ ++r  f++++r++rl+ryggdcyay++vA+G vdlv+e++l+ +Di al+p+ie
  NCBI__GCF_000010525.1:WP_012172788.1 153 GRLEDAILFTTSP-LLMNAADRTLFQSVERDVRLSRYGGDCYAYCMVAAGLVDLVIETGLQDHDIVALVPVIE 224
                                           *************.8********************************************************** PP

                             TIGR02067 216 eAggvitdwkGkeaeeggeavaaanaalhdevlellk 252
                                           +Agg++t+w+G +  +gg++vaa+++a+h+++l++l+
  NCBI__GCF_000010525.1:WP_012172788.1 225 GAGGIVTNWEGGSPVAGGRVVAAGSKAVHEQALKRLN 261
                                           *********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (252 nodes)
Target sequences:                          1  (262 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 14.73
//
[ok]

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

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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