Alignments for a candidate for thrC in Maridesulfovibrio zosterae DSM 11974

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Maridesulfovibrio zosterae DSM 11974

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_027722810.1 H589_RS0115145 threonine synthase

Query= reanno::Miya:8501211
         (492 letters)



>NCBI__GCF_000425265.1:WP_027722810.1
          Length = 483

 Score =  688 bits (1776), Expect = 0.0
 Identities = 333/478 (69%), Positives = 391/478 (81%), Gaps = 1/478 (0%)

Query: 14  FPTARTRMEYVCLGCGERRGIDELLYTCPSCGGVYLLEDLDFDTLAEQRTGPEWRALFDA 73
           FP  R +MEY CLGCG++  IDELLYTCP CG V++LEDL F  L ++ +G EWR +FDA
Sbjct: 7   FPEYRAKMEYHCLGCGKKYDIDELLYTCPECGSVFILEDLTFAEL-KKTSGAEWRNIFDA 65

Query: 74  RAATRTTALRGIFRFYELMAPVLEEEDIVYLGEGNTPIVEAAPVLRDAVGIPFAFKNDGQ 133
           R AT+  +LRGIFRFYEL A V+EE++I+YLGEGNTPIV ++P L +  GI  A+KNDGQ
Sbjct: 66  RCATKKDSLRGIFRFYELFAAVMEEDEILYLGEGNTPIVASSPALNEVTGIKTAYKNDGQ 125

Query: 134 NPSASFKDRGMACAFSYLKALVRKHGWDEVLTVCASTGDTSAAAALYASYVGGPVKSVVL 193
           NPSASFKDRGMACAFSY+ AL+ KH WDE+LTVCASTGDTSAAAALYASY+   VKSVV+
Sbjct: 126 NPSASFKDRGMACAFSYINALLNKHDWDEILTVCASTGDTSAAAALYASYMDSRVKSVVI 185

Query: 194 LPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRILGQES 253
           LP GKVTPQQL+QPLGSGA VLE+PGVFDDCMKVVEHLA+NYRVALLNSKN+WRILGQES
Sbjct: 186 LPQGKVTPQQLAQPLGSGAKVLEVPGVFDDCMKVVEHLADNYRVALLNSKNAWRILGQES 245

Query: 254 YAFEVAQWYGWDMKGQCVFVPIGNAGNVTAIMAGFLKLLRLGVIDALPRVIGVQSHHADP 313
           YAFEVAQWY WD+K +C+FVPIGNAGN+TAIMAGFLKL  L +I  LPRV GVQS HADP
Sbjct: 246 YAFEVAQWYDWDLKDKCIFVPIGNAGNITAIMAGFLKLYELEIITDLPRVFGVQSAHADP 305

Query: 314 VWRYYSQPDPATRTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFIAEGGERAFSVVQV 373
           V+RYYS  DP  R + PV VQPSVAQAAMIGNPVSFPRVK  A++F   GG++AF V+QV
Sbjct: 306 VYRYYSVDDPKEREFKPVKVQPSVAQAAMIGNPVSFPRVKHFAEKFETIGGKKAFQVIQV 365

Query: 374 TEQEIMDAMIRGNRHGHIACTQGGECLAGLIKARELGLVSQGEHAVLDATAHSLKFAGFQ 433
           +EQ+IMD+M+  N +GHIACTQGGEC AGLI+A+ELGL+S+ E AVLD+TAH LKF GFQ
Sbjct: 366 SEQQIMDSMLLANANGHIACTQGGECFAGLIRAKELGLISETESAVLDSTAHQLKFVGFQ 425

Query: 434 DMYFTNSFPPEYGVTPDASLANAPALVVSPEDKARLSPEAYTLAAAKAVVARLGLAKK 491
           DMY+ N+FP EY VTPD S +N P LV++  +K  +    Y   AA  VV+ LGL KK
Sbjct: 426 DMYYQNNFPAEYEVTPDTSRSNKPELVINGTEKDSMPEAEYIAKAANNVVSMLGLEKK 483


Lambda     K      H
   0.320    0.136    0.416 

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: 684
Number of extensions: 18
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: 492
Length of database: 483
Length adjustment: 34
Effective length of query: 458
Effective length of database: 449
Effective search space:   205642
Effective search space used:   205642
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 WP_027722810.1 H589_RS0115145 (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.3051735.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-58  184.6   0.0    1.8e-58  184.2   0.0    1.0  1  NCBI__GCF_000425265.1:WP_027722810.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_027722810.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.2   0.0   1.8e-58   1.8e-58       4     324 ..      81     421 ..      77     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 1.8e-58
                             TIGR00260   4 yreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne. 74 
                                           y+ +  v  e +++ l eg+t+ ++s    +ev++ +   k+++ +P+ +FKDrg   +a ++++++ l n+ 
  NCBI__GCF_000425265.1:WP_027722810.1  81 YELFAAVMeEDEILYLGEGNTPIVASSPALNEVTGIKTAYKNDGQNPSASFKDRG---MACAFSYINALLNKh 150
                                           44455555788999***********999999999977778***************...**********99999 PP

                             TIGR00260  75 .....tvlcAtsGdtgaaaa.ealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvk 141
                                                + +cA++Gdt+aaaa +a +  + vk vv++P+gk+    ++l++ l ++akvl++ G FDd+ ++v+
  NCBI__GCF_000425265.1:WP_027722810.1 151 dwdeiLTVCASTGDTSAAAAlYASYMDSRVKSVVILPQGKVT--PQQLAQPLGSGAKVLEVPGVFDDCMKVVE 221
                                           9***9999*******988763777788899************..9**************************** PP

                             TIGR00260 142 eifedkeklklnsvNsinparieaqktyafeiveqlgkespdk.vvvpvp.sgnfgailkGflekkelg.... 208
                                           +++++ + ++lns N     ri++q +yafe+++ ++++ +dk + vp++ +gn++ai++Gfl++ el     
  NCBI__GCF_000425265.1:WP_027722810.1 222 HLADNYRVALLNSKN---AWRILGQESYAFEVAQWYDWDLKDKcIFVPIGnAGNITAIMAGFLKLYELEiitd 291
                                           ***998888888888...89******************999985779*********************99999 PP

                             TIGR00260 209 lpieklaiaaegaadivrrfl....ksgdlepkedkeTlstAmdignpsnveralelarr..slgnledlkes 275
                                           lp +  ++++  a +++r +     k+++++p + +  +++A  ignp++++r+++ a++  + g  ++ +  
  NCBI__GCF_000425265.1:WP_027722810.1 292 LP-RVFGVQSAHADPVYRYYSvddpKEREFKPVKVQPSVAQAAMIGNPVSFPRVKHFAEKfeTIGGKKAFQVI 363
                                           **.*************99886444477799999999********************77752255555666556 PP

                             TIGR00260 276 vsdeeileaikklaeeegyllephtavavaalkklvekg....vs.....atadpaKF 324
                                            ++e+ + + ++la+ +g ++ + ++   a+l++  e g    +      +ta++ KF
  NCBI__GCF_000425265.1:WP_027722810.1 364 QVSEQQIMDSMLLANANGHIACTQGGECFAGLIRAKELGliseTEsavldSTAHQLKF 421
                                           66677777778888888888889999********999996544114566677777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (483 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 31.24
//
[ok]

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