GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Shewanella amazonensis SB2B

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate 6938618 Sama_2721 glycine cleavage system aminomethyltransferase T (RefSeq)

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__SB2B:6938618
          Length = 364

 Score =  521 bits (1342), Expect = e-152
 Identities = 254/361 (70%), Positives = 301/361 (83%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           MA +T L+ +H    A+MVDFHGW MPL+YGSQI+EHHAVR DAGMFDVSHMT+VD+ G+
Sbjct: 1   MANKTVLFSKHLESNAKMVDFHGWNMPLNYGSQIEEHHAVRRDAGMFDVSHMTVVDVEGA 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
             R FLR LLAND+AKLT  GKALY GMLN  GGVIDDLI YY ++  +R+VVNSATREK
Sbjct: 61  DARAFLRKLLANDIAKLTVPGKALYGGMLNHDGGVIDDLITYYLSDTQYRVVVNSATREK 120

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DL+WI + A+ F + IT R +L+MIAVQGPNA+AKAAT+F   Q  AVEGMKPFFG QAG
Sbjct: 121 DLAWIGEQAKGFDVTITERPELAMIAVQGPNAKAKAATVFTAEQNAAVEGMKPFFGKQAG 180

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
            LFIATTGYTGEAGYEI +P  +A   W+AL++AGV+PCGLGARDTLRLEAGMNLYGQ+M
Sbjct: 181 SLFIATTGYTGEAGYEIIVPEAEAEALWQALLDAGVQPCGLGARDTLRLEAGMNLYGQDM 240

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRF 300
           DE+++PLAANMGWTIAWEPADRDFIGREALE  +  G++KLVGLVM EKGVLR+++PV F
Sbjct: 241 DESVNPLAANMGWTIAWEPADRDFIGREALEAIKAKGSDKLVGLVMEEKGVLRHDMPVFF 300

Query: 301 TDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNG 360
           TDA G +H+G+ITSGTFSPTLGYSIA+ARVP  IGETA V++R + + V+V  P FVRNG
Sbjct: 301 TDANGVEHQGVITSGTFSPTLGYSIAMARVPGAIGETAEVEMRKKRVTVRVIAPSFVRNG 360

Query: 361 K 361
           K
Sbjct: 361 K 361


Lambda     K      H
   0.320    0.136    0.402 

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: 477
Number of extensions: 12
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 6938618 Sama_2721 (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.810162.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                     -----------
     1e-144  467.9   0.1   1.1e-144  467.7   0.1    1.0  1  FitnessBrowser__SB2B:6938618  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__SB2B:6938618  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.7   0.1  1.1e-144  1.1e-144       2     362 .]       3     359 ..       2     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 467.7 bits;  conditional E-value: 1.1e-144
                     TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk.Gka 81 
                                   ++t L+  h e  +k+vdf+Gw++P++y+s+ieeh+avr +aG+fDvshm+ v+++G ++++fL++llanD+++Lt+ Gka
  FitnessBrowser__SB2B:6938618   3 NKTVLFSKHLESNAKMVDFHGWNMPLNYGSQIEEHHAVRRDAGMFDVSHMTVVDVEGADARAFLRKLLANDIAKLTVpGKA 83 
                                   79**************************************************************************99*** PP

                     TIGR00528  82 qysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP....kaktiledl 158
                                   +y ++ln +GGv+DDli y+ ++  ++++vvn+at+ekDl+w+ e+++++   +t + e++++a+qGP    ka+t++   
  FitnessBrowser__SB2B:6938618  84 LYGGMLNHDGGVIDDLITYYLSDT-QYRVVVNSATREKDLAWIGEQAKGFDVTITERPELAMIAVQGPnakaKAATVFTAE 163
                                   *********************999.9******************************************9999999****** PP

                     TIGR00528 159 ldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGq 239
                                   +++aveg+k+ff+ q++ l     +ia+tGytGe+G+ei+v++ +a  lw++l++a gv+P+GLgarDtLrleagm+LyGq
  FitnessBrowser__SB2B:6938618 164 QNAAVEGMKPFFGKQAGSL-----FIATTGYTGEAGYEIIVPEAEAEALWQALLDA-GVQPCGLGARDTLRLEAGMNLYGQ 238
                                   *******************.....********************************.************************ PP

                     TIGR00528 240 eldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvllt..ngekevGivtsGtls 318
                                   ++de++ Pl+a++gw++++e++++dfiGr++le  k++g++k lvGl+m ekg++r++++v++t  ng ++ G++tsGt+s
  FitnessBrowser__SB2B:6938618 239 DMDESVNPLAANMGWTIAWEPADRDFIGREALEAIKAKGSDK-LVGLVMEEKGVLRHDMPVFFTdaNGVEHQGVITSGTFS 318
                                   ***************************************998.********************9666779*********** PP

                     TIGR00528 319 PtLgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                   PtLg++ia+a+v+     iG+++eve+r+k v ++v+ + fvr+
  FitnessBrowser__SB2B:6938618 319 PTLGYSIAMARVP---GAIGETAEVEMRKKRVTVRVIAPSFVRN 359
                                   *************...89***********************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.68
//
[ok]

This GapMind analysis is from Apr 09 2024. 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