GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Thiohalospira halophila HL 3

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate WP_093428263.1 BM272_RS08005 glycine cleavage system aminomethyltransferase GcvT

Query= reanno::Koxy:BWI76_RS23880
         (364 letters)



>NCBI__GCF_900112605.1:WP_093428263.1
          Length = 366

 Score =  377 bits (969), Expect = e-109
 Identities = 193/366 (52%), Positives = 247/366 (67%), Gaps = 10/366 (2%)

Query: 3   QQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGSRI 62
           ++TPL ++H   GA++ DF+GW +P+HYGSQ++EHH VR +AGMFDVSHM +VD  G   
Sbjct: 4   KRTPLHDKHVAAGAKLADFYGWELPVHYGSQVEEHHHVRNEAGMFDVSHMNVVDIEGEGA 63

Query: 63  REFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREKDL 122
            +FLRYLLANDVAKL  PGKALYS M    GGV DDLIVY + + ++R ++N+AT +KD+
Sbjct: 64  TDFLRYLLANDVAKLKTPGKALYSCMCNPEGGVEDDLIVYRMHDTWYRAILNAATHDKDM 123

Query: 123 AWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAGDL 182
           AW+ Q    +   +  R DL+L+AVQGP+A+E+A     +    A + +KPF       L
Sbjct: 124 AWLEQHIAGFACTLCERTDLALVAVQGPKARERALDALGENGAFAAD-LKPFQAAGDDRL 182

Query: 183 FIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEMDE 242
           FI  TGYTGE G+EI++PNE+    W  L  AG++P G GARDTLRLEAGM LY  EMDE
Sbjct: 183 FIGRTGYTGEDGFEISVPNERIAGLWDELEAAGIQPVGFGARDTLRLEAGMALYSHEMDE 242

Query: 243 GVSPLAANMGWTIAWEPTDRDFIGREALEMQREKG-TEQLVGLVMTEKGVLRGGLPVRFS 301
             SPL A + WT+A+EP DRDF+GR ALE QRE G   + VGLV+ ++GVLR G  V  +
Sbjct: 243 STSPLEAGLAWTVAFEPADRDFLGRAALERQREAGVAREQVGLVLADRGVLRDGQTVHCA 302

Query: 302 DADGNQKEGIITSGTFSPTLGYSIALARVPEGIGET---AVVQIRNREMPVKVTKPVFVR 358
             D     GI TSGTFSPTLG +IALA VP G  E      V +RN+ +   V KP FVR
Sbjct: 303 GGD-----GITTSGTFSPTLGRAIALALVPAGTAEAGGRCEVAVRNKRLSAAVVKPPFVR 357

Query: 359 NGKAVV 364
           NG+A V
Sbjct: 358 NGQARV 363


Lambda     K      H
   0.320    0.137    0.407 

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: 438
Number of extensions: 16
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: 364
Length of database: 366
Length adjustment: 30
Effective length of query: 334
Effective length of database: 336
Effective search space:   112224
Effective search space used:   112224
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: 49 (23.5 bits)

Align candidate WP_093428263.1 BM272_RS08005 (glycine cleavage system aminomethyltransferase GcvT)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

# 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.carbon/TIGR00528.hmm
# target sequence database:        /tmp/gapView.2642567.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00528  [M=362]
Accession:   TIGR00528
Description: gcvT: glycine cleavage system T protein
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-131  423.1   0.0   4.8e-131  422.9   0.0    1.0  1  NCBI__GCF_900112605.1:WP_093428263.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093428263.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.9   0.0  4.8e-131  4.8e-131       1     362 []       3     358 ..       3     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 422.9 bits;  conditional E-value: 4.8e-131
                             TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDv 73 
                                           lkrtpL+d h+  g+kl df GwelPv+y+s++eeh+ vr++aG+fDvshm  v+++G+ + +fL++llanDv
  NCBI__GCF_900112605.1:WP_093428263.1   3 LKRTPLHDKHVAAGAKLADFYGWELPVHYGSQVEEHHHVRNEAGMFDVSHMNVVDIEGEGATDFLRYLLANDV 75 
                                           69*********************************************************************** PP

                             TIGR00528  74 daLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeislla 145
                                           ++L + Gka+ys ++n++GGv DDlivy+  +   ++ ++naat +kD++wl++h+++++   + + +++l+a
  NCBI__GCF_900112605.1:WP_093428263.1  76 AKLKTpGKALYSCMCNPEGGVEDDLIVYRMHDT-WYRAILNAATHDKDMAWLEQHIAGFACTLCERTDLALVA 147
                                           ***555***********************9998.*************************************** PP

                             TIGR00528 146 lqGPkakt.iledlldkaveg..lkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveay 215
                                           +qGPka++  l+ l ++ + +  lk+f    +  l     +i rtGytGedGfei+v+ne+ + lw +l +a 
  NCBI__GCF_900112605.1:WP_093428263.1 148 VQGPKARErALDALGENGAFAadLKPFQAAGDDRL-----FIGRTGYTGEDGFEISVPNERIAGLWDELEAA- 214
                                           ******76266777665543335****99977777.....*****************************999. PP

                             TIGR00528 216 gvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlem 288
                                           g++P+G+garDtLrleagmaLy +e+de+++Pleagl w+v+ e++++df+Gra+le q+e g+ +  vGl++
  NCBI__GCF_900112605.1:WP_093428263.1 215 GIQPVGFGARDTLRLEAGMALYSHEMDESTSPLEAGLAWTVAFEPADRDFLGRAALERQREAGVAREQVGLVL 287
                                           ************************************************************************* PP

                             TIGR00528 289 lekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                            ++g++r++  v  + g    Gi tsGt+sPtLg +iala+v+ ++++ G + ev vrnk +++ vvk++fvr
  NCBI__GCF_900112605.1:WP_093428263.1 288 ADRGVLRDGQTVHCAGG---DGITTSGTFSPTLGRAIALALVPAGTAEAGGRCEVAVRNKRLSAAVVKPPFVR 357
                                           ************99666...8***************************************************9 PP

                             TIGR00528 362 s 362
                                           +
  NCBI__GCF_900112605.1:WP_093428263.1 358 N 358
                                           6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (366 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: 23.73
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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