Alignments for a candidate for thrC in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Herbaspirillum seropedicae SmR1

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate HSERO_RS10470 HSERO_RS10470 threonine synthase

Query= BRENDA::Q2SWH9
         (483 letters)



>FitnessBrowser__HerbieS:HSERO_RS10470
          Length = 486

 Score =  698 bits (1802), Expect = 0.0
 Identities = 350/487 (71%), Positives = 401/487 (82%), Gaps = 7/487 (1%)

Query: 1   MNYISTRGAGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFEI 60
           M Y+STRG       +FS+ILLGGLA DGGLYLP++YPQVS  EL +WR L YADLAFE+
Sbjct: 1   MQYVSTRGHAATP--SFSEILLGGLAPDGGLYLPAQYPQVSGAELDQWRKLSYADLAFEV 58

Query: 61  LSKFCDDIAAADLRAITRRTYTADVYRHARRGGNAADITPLTTLGTENGAPVSLLELSNG 120
           L KF  DI  ADL+A+  +TYTADVYR+ R G +AA+ITPL TL  + G  + L  LSNG
Sbjct: 59  LRKFATDIPEADLKALAHKTYTADVYRNTRAGEHAAEITPLRTLEEQGGKKLVLQSLSNG 118

Query: 121 PTLAFKDMAMQLLGNLFEYTLAKHGETLNILGATSGDTGSAAEYAMRGKEGVRVFMLSPH 180
           PTLAFKDMAMQLLGNLFEY LAK G  LNI+GATSGDTGSAAEYAMRGK+G+RVFMLSPH
Sbjct: 119 PTLAFKDMAMQLLGNLFEYALAKQGAELNIVGATSGDTGSAAEYAMRGKKGIRVFMLSPH 178

Query: 181 KKMSAFQTAQMYSLQDPNIFNLAVNGVFDDCQDIVKAVSNDHAFKAQQKIGTVNSINWAR 240
           KKMSAFQTAQM+SLQDPNIFNLA+ GVFDDCQDIVKA+SND  +KA +KIGTVNSINWAR
Sbjct: 179 KKMSAFQTAQMFSLQDPNIFNLAIEGVFDDCQDIVKAISNDLEYKAAKKIGTVNSINWAR 238

Query: 241 VVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNENDV 300
           VVAQVVYYF+GY AAT SN+++VSFTVPSGNFGN+CAGHIARMMGLPI+KLVVATNENDV
Sbjct: 239 VVAQVVYYFRGYLAATTSNEQKVSFTVPSGNFGNICAGHIARMMGLPIDKLVVATNENDV 298

Query: 301 LDEFFRTGAYRVRSAQDTYHTSSPSMDISKASNFERFVFDLLGRDPARVVQLFRDVEQKG 360
           LDEFFRTG YRVR + +TYHTSSPSMDISKASNFERFV+DLLGRD ARV  LF  VE  G
Sbjct: 299 LDEFFRTGIYRVRKSAETYHTSSPSMDISKASNFERFVYDLLGRDSARVKDLFHKVETAG 358

Query: 361 GFDLAA-----SGDFARVAEFGFVSGRSTHADRIATIRDVFERYRTMIDTHTADGLKVAR 415
           GFDL+        +F  V ++GF SGRSTHADR+ TIR   + Y   +DTHTADG+KVAR
Sbjct: 359 GFDLSGQAGSDGNEFTSVIQYGFASGRSTHADRLETIRFAEKTYGITVDTHTADGIKVAR 418

Query: 416 EHLRPGVPMVVLETAQPIKFGESIREALGQEPSRPAAFDGLEALPQRFEVVDANAQQVKD 475
           EHL PGV M+VLETA P KF E+IREALG++  RPA F+ +EALPQRFEV+ A+A +VK 
Sbjct: 419 EHLTPGVTMIVLETALPAKFNETIREALGRDADRPAGFENIEALPQRFEVMPADAARVKA 478

Query: 476 FIAAHTG 482
           ++A HTG
Sbjct: 479 YVAQHTG 485


Lambda     K      H
   0.320    0.135    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: 735
Number of extensions: 25
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: 483
Length of database: 486
Length adjustment: 34
Effective length of query: 449
Effective length of database: 452
Effective search space:   202948
Effective search space used:   202948
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate HSERO_RS10470 HSERO_RS10470 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# 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/TIGR00260.hmm
# target sequence database:        /tmp/gapView.9623.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    1.3e-74  237.3   0.1    1.7e-74  237.0   0.1    1.1  1  lcl|FitnessBrowser__HerbieS:HSERO_RS10470  HSERO_RS10470 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS10470  HSERO_RS10470 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.0   0.1   1.7e-74   1.7e-74      33     333 ..     103     447 ..      60     453 .. 0.87

  Alignments for each domain:
  == domain 1  score: 237.0 bits;  conditional E-value: 1.7e-74
                                  TIGR00260  33 eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanv 98 
                                                ee g+++l ++ l+ gPtlaFKD+++q +++l+++al ++ +   +++AtsGdtg+aa +a++gk+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS10470 103 EEQGGKKLVLQSLSNGPTLAFKDMAMQLLGNLFEYALAKQGAelNIVGATSGDTGSAAEYAMRGKKGI 170
                                                3334489***************************99766555579*********************** PP

                                  TIGR00260  99 kvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinpar 162
                                                +v++L P+ k+s     +++   + n+  lai+G FDd+qd+vk+i +d e   + k++ vNsin+ar
  lcl|FitnessBrowser__HerbieS:HSERO_RS10470 171 RVFMLSPHKKMSAFqTAQMFSLQDPNIFNLAIEGVFDDCQDIVKAISNDLEykaAKKIGTVNSINWAR 238
                                                **************99*******************************944445599************ PP

                                  TIGR00260 163 ieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflk 230
                                                + aq++y+f    +    +++kv + vpsgnfg+i +G   ++++glpi+kl +a++++ d++++f +
  lcl|FitnessBrowser__HerbieS:HSERO_RS10470 239 VVAQVVYYFRGYLAATTSNEQKVSFTVPSGNFGNICAG-HIARMMGLPIDKLVVATNEN-DVLDEFFR 304
                                                *****7777665555559999*****************.6667777************9.******** PP

                                  TIGR00260 231 sg.dlepkedk..eTlstAmdignpsnverale.larrslgnledlke.................... 274
                                                +g + + k+    +T s++mdi++ sn+er +  l  r  + ++dl +                    
  lcl|FitnessBrowser__HerbieS:HSERO_RS10470 305 TGiYRVRKSAEtyHTSSPSMDISKASNFERFVYdLLGRDSARVKDLFHkvetaggfdlsgqagsdgne 372
                                                **65444444357899**************8877999999999999768999**************** PP

                                  TIGR00260 275 ............svsdeeileaikklaeeegyllephtavavaalkklvekg.vs...atadpaKFee 326
                                                            + + ++ le+i+ + ++ g+++++hta ++++ ++ +  g +     ta paKF+e
  lcl|FitnessBrowser__HerbieS:HSERO_RS10470 373 ftsviqygfasgRSTHADRLETIRFAEKTYGITVDTHTADGIKVAREHLTPGvTMivlETALPAKFNE 440
                                                ****************************************************6225679********9 PP

                                  TIGR00260 327 vvealtg 333
                                                ++   +g
  lcl|FitnessBrowser__HerbieS:HSERO_RS10470 441 TIREALG 447
                                                9985444 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (486 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: 8.90
//
[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