GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Shewanella loihica PV-4

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate 5210636 Shew_3064 glycine cleavage system aminomethyltransferase T (RefSeq)

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



>FitnessBrowser__PV4:5210636
          Length = 364

 Score =  514 bits (1323), Expect = e-150
 Identities = 251/361 (69%), Positives = 294/361 (81%)

Query: 1   MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60
           MA +T LF +H    A+MVDFHGW MPL+YGSQI+EHH VR DAGMFDVSHMT+VD  G+
Sbjct: 1   MANKTVLFNKHLEANAKMVDFHGWDMPLNYGSQIEEHHVVRQDAGMFDVSHMTVVDVTGA 60

Query: 61  RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK 120
              +FLR LLANDVAKL VPGKALY GML  + GVIDDLI Y+LS+ ++R+VVNSATREK
Sbjct: 61  EACDFLRKLLANDVAKLKVPGKALYGGMLDHNAGVIDDLITYYLSDTHYRIVVNSATREK 120

Query: 121 DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG 180
           DLAWI +Q + Y + +T R +L++IAVQGP AK KAA +FTD Q  AVEGMKPFFGVQ+G
Sbjct: 121 DLAWITEQVKGYDVTVTERPELAMIAVQGPNAKAKAAAVFTDEQNAAVEGMKPFFGVQSG 180

Query: 181 DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM 240
            LFIATTGYTGEAGYEI +P  +A   W+ LLD GVKPCGLGARDTLRLEAGMNLYGQ+M
Sbjct: 181 SLFIATTGYTGEAGYEIIVPEAEAEALWQALLDNGVKPCGLGARDTLRLEAGMNLYGQDM 240

Query: 241 DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRF 300
           DE V+PLAANMGWTIAWEP DRDFIGREAL   +  GT++LVGLVM  KGVLR G+PV F
Sbjct: 241 DESVNPLAANMGWTIAWEPEDRDFIGREALAAIKAAGTDKLVGLVMEAKGVLRTGMPVFF 300

Query: 301 SDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRNG 360
           +DADG +++G ITSGTFSPTLGYSIA+ARVP  +G+ A V++R + +PVKV  P FVRNG
Sbjct: 301 TDADGVEQQGAITSGTFSPTLGYSIAMARVPNSVGDVAEVEMRKKRVPVKVIAPSFVRNG 360

Query: 361 K 361
           K
Sbjct: 361 K 361


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: 502
Number of extensions: 13
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: 364
Length of database: 364
Length adjustment: 29
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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 5210636 Shew_3064 (glycine cleavage system aminomethyltransferase T (RefSeq))
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.6994.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.2e-142  459.7   0.1   3.6e-142  459.5   0.1    1.0  1  lcl|FitnessBrowser__PV4:5210636  Shew_3064 glycine cleavage syste


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210636  Shew_3064 glycine cleavage system aminomethyltransferase T (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.5   0.1  3.6e-142  3.6e-142       2     362 .]       3     359 ..       2     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 459.5 bits;  conditional E-value: 3.6e-142
                        TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk. 78 
                                      ++t L++ h e  +k+vdf+Gw +P++y+s+ieeh+ vr++aG+fDvshm+ v+++G ++ +fL++llanDv++L + 
  lcl|FitnessBrowser__PV4:5210636   3 NKTVLFNKHLEANAKMVDFHGWDMPLNYGSQIEEHHVVRQDAGMFDVSHMTVVDVTGAEACDFLRKLLANDVAKLKVp 80 
                                      79*************************************************************************988 PP

                        TIGR00528  79 GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP....kak 152
                                      Gka+y ++l  + Gv+DDli y+ ++  ++++vvn+at+ekDl+w++e++++     t + e++++a+qGP    ka+
  lcl|FitnessBrowser__PV4:5210636  81 GKALYGGMLDHNAGVIDDLITYYLSDT-HYRIVVNSATREKDLAWITEQVKGYDVTVTERPELAMIAVQGPnakaKAA 157
                                      ************************999.*******************************************9999999 PP

                        TIGR00528 153 tiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrl 230
                                      +++ d +++aveg+k+ff+vq + l     +ia+tGytGe+G+ei+v++ +a  lw++l+++ gvkP+GLgarDtLrl
  lcl|FitnessBrowser__PV4:5210636 158 AVFTDEQNAAVEGMKPFFGVQSGSL-----FIATTGYTGEAGYEIIVPEAEAEALWQALLDN-GVKPCGLGARDTLRL 229
                                      *************************.....********************************.*************** PP

                        TIGR00528 231 eagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvllt..nge 306
                                      eagm+LyGq++de++ Pl+a++gw++++e++++dfiGr++l   k+ gt+k lvGl+m +kg++r +++v++t  +g 
  lcl|FitnessBrowser__PV4:5210636 230 EAGMNLYGQDMDESVNPLAANMGWTIAWEPEDRDFIGREALAAIKAAGTDK-LVGLVMEAKGVLRTGMPVFFTdaDGV 306
                                      *************************************************99.********************966677 PP

                        TIGR00528 307 kevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                      ++ G +tsGt+sPtLg++ia+a+v+   + +G+++eve+r+k v++kv+ + fvr+
  lcl|FitnessBrowser__PV4:5210636 307 EQQGAITSGTFSPTLGYSIAMARVP---NSVGDVAEVEMRKKRVPVKVIAPSFVRN 359
                                      99***********************...99***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (364 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: 00:00:00.01
# Mc/sec: 9.28
//
[ok]

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

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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:

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