Alignments for a candidate for hisN in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisN in Sinorhizobium meliloti 1021

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate SMc04042 SMc04042 monophosphatase

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



>FitnessBrowser__Smeli:SMc04042
          Length = 259

 Score =  234 bits (596), Expect = 2e-66
 Identities = 121/247 (48%), Positives = 157/247 (63%), Gaps = 1/247 (0%)

Query: 1   MADAARQAILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILGEEF 60
           +ADAA+   +P FR  G    NKL+ GFDPVT ADR+AE ++R+++    PE  ILGEE 
Sbjct: 11  LADAAKAETMPRFR-VGTSVLNKLEGGFDPVTEADRSAEASIRALIESSFPEHGILGEEH 69

Query: 61  GETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPE 120
           G         WV+DPIDGTR FISG P WG LI L       +G++DQP+ GERF    E
Sbjct: 70  GNIGLDRELVWVIDPIDGTRAFISGLPVWGTLIGLYRNGKAVMGLMDQPFTGERFFADGE 129

Query: 121 GASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDCYA 180
            A   GP G   L TR   +LS+A LFTT P + T   +  F+ +  +VRL RYG DCYA
Sbjct: 130 KALYRGPDGERVLATRPCHALSDAVLFTTSPHLYTGELKERFEALQEKVRLFRYGCDCYA 189

Query: 181 YALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELHA 240
           +ALLAAG  DLV+E GL  YD+   I +I+ AGG++T+WQG PA  GG+++AA + ELHA
Sbjct: 190 FALLAAGHVDLVVECGLKPYDVGGLIPLIEQAGGIITDWQGGPAEMGGEIIAAGSRELHA 249

Query: 241 AALALIQ 247
            AL  ++
Sbjct: 250 QALEALK 256


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: 222
Number of extensions: 11
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: 250
Length of database: 259
Length adjustment: 24
Effective length of query: 226
Effective length of database: 235
Effective search space:    53110
Effective search space used:    53110
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 SMc04042 SMc04042 (monophosphatase)
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.3896.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.2e-102  327.8   0.0   2.5e-102  327.7   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc04042  SMc04042 monophosphatase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04042  SMc04042 monophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.7   0.0  2.5e-102  2.5e-102       2     252 .]       5     256 ..       4     256 .. 0.98

  Alignments for each domain:
  == domain 1  score: 327.7 bits;  conditional E-value: 2.5e-102
                           TIGR02067   2 lalalelaeaageailkyfrasdlkvdkksdk.tpVteADraaEeaireliaakfPddgilGEEfgeeeedaeyv 75 
                                         ++++++la+aa+++++++fr  +++ +k +   +pVteADr+aE+ ir+li+++fP++gilGEE+g++  d+e v
  lcl|FitnessBrowser__Smeli:SMc04042   5 RTFFDRLADAAKAETMPRFRVGTSVLNKLEGGfDPVTEADRSAEASIRALIESSFPEHGILGEEHGNIGLDRELV 79 
                                         6899************************99999****************************************** PP

                           TIGR02067  76 WvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallng.gerelrvsevaklsdAv 149
                                         Wv+DPiDGT++Fi+G+PvwgtLi+L+++gk+v+G+++qP++gerf+a+ +++ ++ + ger l+++ +++lsdAv
  lcl|FitnessBrowser__Smeli:SMc04042  80 WVIDPIDGTRAFISGLPVWGTLIGLYRNGKAVMGLMDQPFTGERFFADGEKALYRGPdGERVLATRPCHALSDAV 154
                                         *******************************************************98667*************** PP

                           TIGR02067 150 lvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipiieeAggvitdw 224
                                         l+ttsp +l + e +e+fe+l++k+rl ryg+dcya+al+A+G+vdlvve++l+pyD+  lip+ie+Agg+itdw
  lcl|FitnessBrowser__Smeli:SMc04042 155 LFTTSP-HLYTGELKERFEALQEKVRLFRYGCDCYAFALLAAGHVDLVVECGLKPYDVGGLIPLIEQAGGIITDW 228
                                         ******.9******************************************************************* PP

                           TIGR02067 225 kGkeaeeggeavaaanaalhdevlellk 252
                                         +G +ae+gge++aa++++lh+++le+lk
  lcl|FitnessBrowser__Smeli:SMc04042 229 QGGPAEMGGEIIAAGSRELHAQALEALK 256
                                         *************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (252 nodes)
Target sequences:                          1  (259 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.67
//
[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