Alignments for a candidate for thrC in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Acidovorax sp. GW101-3H11

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate Ac3H11_1505 Threonine synthase (EC 4.2.3.1)

Query= BRENDA::Q2SWH9
         (483 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1505
          Length = 481

 Score =  604 bits (1558), Expect = e-177
 Identities = 325/487 (66%), Positives = 375/487 (77%), Gaps = 20/487 (4%)

Query: 1   MNYISTRGAGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTL----PYADL 56
           M Y+STRG    +R  F DILL GLA DGGLYLP  YP+++A  L + R       YA+L
Sbjct: 1   MKYLSTRGHA--DRKQFCDILLEGLAPDGGLYLPETYPKITAAALTKLRKAYHEQGYAEL 58

Query: 57  AFEILSKFCDDIAAADLRAITRRTYTADVYRHARRGGNAADITPLTTLGTENGAPVSLLE 116
           AF+ILS + DDI AADL+AI  +TYTA+V+          +I PL  L  E+G  + L  
Sbjct: 59  AFQILSLYIDDIPAADLKAICAKTYTAEVF-------GTGEIVPLRHL--EDG--LWLEA 107

Query: 117 LSNGPTLAFKDMAMQLLGNLFEYTLAKHGETLNILGATSGDTGSAAEYAMRGKEGVRVFM 176
           LSNGPTLAFKDMAMQLLGNLFEY L + GE LNILGATSGDTGSAAEYAMRGKEGVRVFM
Sbjct: 108 LSNGPTLAFKDMAMQLLGNLFEYELGRRGEQLNILGATSGDTGSAAEYAMRGKEGVRVFM 167

Query: 177 LSPHKKMSAFQTAQMYSLQDPNIFNLAVNGVFDDCQDIVKAVSNDHAFKAQQKIGTVNSI 236
            SPH +MSAFQ AQM+SLQD NI N+A+ GVFDDCQDIVKAVSNDHAFKA+ KIGTVNSI
Sbjct: 168 TSPHGRMSAFQQAQMFSLQDENIHNIAIEGVFDDCQDIVKAVSNDHAFKAKYKIGTVNSI 227

Query: 237 NWARVVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATN 296
           NWAR++AQVVYYF GY  AT +N+++VSFTVPSGNFGN+CAGH+ARMMGLPI KLVVATN
Sbjct: 228 NWARLLAQVVYYFAGYIQATETNNQKVSFTVPSGNFGNICAGHVARMMGLPIAKLVVATN 287

Query: 297 ENDVLDEFFRTGAYRVRSAQDTYHTSSPSMDISKASNFERFVFDLLGRDPARVVQLFRDV 356
           ENDVLDEFFRTG YRVR + DT+ TSSPSMDISKASNFERF+FDLLGR+  R   LF   
Sbjct: 288 ENDVLDEFFRTGVYRVRGSADTHETSSPSMDISKASNFERFIFDLLGRNGQRTKALFSAA 347

Query: 357 EQK-GGFDLAASGDFARVA-EFGFVSGRSTHADRIATIRDVFERYRTMIDTHTADGLKVA 414
            Q  G FDL+A   FA  A ++GF SG+STHADR+ATI+D FER+   IDTHTADG+KVA
Sbjct: 348 LQTYGRFDLSADPLFADAAKKYGFESGKSTHADRLATIKDTFERHGVTIDTHTADGVKVA 407

Query: 415 REHLRPG-VPMVVLETAQPIKFGESIREALGQEPSRPAAFDGLEALPQRFEVVDANAQQV 473
           REH     VPM+VLETA PIKF E+I EALG  P RPA F G+E LP+R  V+ A+ +QV
Sbjct: 408 REHHSDAKVPMIVLETALPIKFAETIIEALGHAPERPAKFAGIEDLPKRVHVMPADVEQV 467

Query: 474 KDFIAAH 480
           K +I  H
Sbjct: 468 KAYIERH 474


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: 707
Number of extensions: 22
Number of successful extensions: 5
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: 481
Length adjustment: 34
Effective length of query: 449
Effective length of database: 447
Effective search space:   200703
Effective search space used:   200703
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 Ac3H11_1505 (Threonine synthase (EC 4.2.3.1))
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.7412.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    4.5e-75  238.8   0.0    5.9e-75  238.5   0.0    1.1  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1505  Threonine synthase (EC 4.2.3.1)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1505  Threonine synthase (EC 4.2.3.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.5   0.0   5.9e-75   5.9e-75      33     333 ..      97     438 ..      61     444 .. 0.86

  Alignments for each domain:
  == domain 1  score: 238.5 bits;  conditional E-value: 5.9e-75
                                        TIGR00260  33 eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaeal 92 
                                                      ++++   l++  l+ gPtlaFKD+++q +++l+++ l++  e   +l+AtsGdtg+aa +a+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1505  97 RHLED-GLWLEALSNGPTLAFKDMAMQLLGNLFEYELGRRGEqlNILGATSGDTGSAAEYAM 157
                                                      45555.899999***********************9988777689***************** PP

                                        TIGR00260  93 agkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...kl 150
                                                      +gk++v+v++  P+g++s   + +++   +en++ +ai+G FDd+qd+vk++ +d+    k+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1505 158 RGKEGVRVFMTSPHGRMSAFqQAQMFSLQDENIHNIAIEGVFDDCQDIVKAVSNDHAfkaKY 219
                                                      *****************************************************9666677** PP

                                        TIGR00260 151 klnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpie 212
                                                      k++ vNsin+ar++aq++y+f    q  + +++kv + vpsgnfg+i +G   ++++glpi+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1505 220 KIGTVNSINWARLLAQVVYYFAGYIQATETNNQKVSFTVPSGNFGNICAGH-VARMMGLPIA 280
                                                      *****************8888666666669999*****************5.556666**** PP

                                        TIGR00260 213 klaiaaegaadivrrflksg.dlepkedk..eTlstAmdignpsnverale.larrslgnle 270
                                                      kl +a++++ d++++f ++g + +  +    eT s++mdi++ sn+er  + l  r+++  +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1505 281 KLVVATNEN-DVLDEFFRTGvYRVRGSADthETSSPSMDISKASNFERFIFdLLGRNGQRTK 341
                                                      ********9.**********64433332247*****************9998999*999999 PP

                                        TIGR00260 271 dlke.............................svsdeeileaikklaeeegyllephtava 303
                                                      +l +                             + + ++ l +ik   e++g+++++hta +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1505 342 ALFSaalqtygrfdlsadplfadaakkygfesgKSTHADRLATIKDTFERHGVTIDTHTADG 403
                                                      99779****************************999************************** PP

                                        TIGR00260 304 vaalkklvekg...vs..atadpaKFeevvealtg 333
                                                      v++ ++ + +    +    ta p KF+e++   +g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1505 404 VKVAREHHSDAkvpMIvlETALPIKFAETIIEALG 438
                                                      *****999988655115699999999998875555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (481 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.28
//
[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