GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Sinorhizobium meliloti 1021

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate SMc02047 SMc02047 glycine cleavage system aminomethyltransferase T

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1866
         (374 letters)



>FitnessBrowser__Smeli:SMc02047
          Length = 379

 Score =  416 bits (1068), Expect = e-121
 Identities = 221/375 (58%), Positives = 265/375 (70%), Gaps = 9/375 (2%)

Query: 6   LLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIRLTGA 65
           L  TPLHALH+ LGARMVPFAGYDMPVQYP GV+KEH HTR  AGLFDVSHMGQI +   
Sbjct: 7   LKHTPLHALHLSLGARMVPFAGYDMPVQYPEGVLKEHLHTRAAAGLFDVSHMGQIVVRPK 66

Query: 66  N-----AAKALETLVPVDIIDLPVGMQRYAMFTNATGGILDDLMVANLGNDELFLVVNAA 120
           +     AA ALE LVP D++ L  G QRY +FTNA GGILDDLM+ N G D LFLVVNAA
Sbjct: 67  SGKIEDAALALEKLVPADVLGLAEGRQRYGLFTNAAGGILDDLMIVNRG-DHLFLVVNAA 125

Query: 121 CKDQDLAHLRKHIGDQCTIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFARVKL 180
           CKD DLAHL+  +G  C +  L  +RAL+ALQGP A  VL  L  +V+ M FM      L
Sbjct: 126 CKDADLAHLKDGLGSVCDVTML-TDRALIALQGPRAGAVLCELWADVSSMRFMDVTEADL 184

Query: 181 LGVDCFVSRSGYTGEDGFEISVPATNAEALARALLAEAEVAAIGLGARDSLRLEAGLCLY 240
             V C +SRSGYTGEDGFEIS+PA  A  + + LL   +V  IGLGARDSLRLEAGLCLY
Sbjct: 185 HDVSCIISRSGYTGEDGFEISIPAEAAVDVTQRLLEHPDVLPIGLGARDSLRLEAGLCLY 244

Query: 241 GHDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQAGVSRKRVGLLPQERT 300
           G+D++T+T+PIEA L WAI K RRA G RAGGFPGA  + A+   GVSR+RVGL P+ R 
Sbjct: 245 GNDIDTNTSPIEAGLEWAIQKSRRAGGERAGGFPGAGRILAELTDGVSRRRVGLRPEGRA 304

Query: 301 PVREGAEIV--NEAGDIIGSVCSGGFGPTLGGPLAMGYVDSAYIALDTPVWAIVRGKKVP 358
           PVR  A +    E     G+V SGGFGP++ GP+AMGYVD+ +  + T ++A VRGK +P
Sbjct: 305 PVRGNANLFADEEGRTAAGTVTSGGFGPSVDGPVAMGYVDAEHAEVGTRLFAEVRGKYLP 364

Query: 359 LLVSKMPFVPQRYYR 373
           + V+ +PF+ Q Y R
Sbjct: 365 IAVTALPFIKQTYKR 379


Lambda     K      H
   0.321    0.138    0.405 

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: 484
Number of extensions: 25
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: 374
Length of database: 379
Length adjustment: 30
Effective length of query: 344
Effective length of database: 349
Effective search space:   120056
Effective search space used:   120056
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: 50 (23.9 bits)

Align candidate SMc02047 SMc02047 (glycine cleavage system aminomethyltransferase T)
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.11182.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.6e-104  333.1   0.0   1.1e-103  332.9   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02047  SMc02047 glycine cleavage system


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02047  SMc02047 glycine cleavage system aminomethyltransferase T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.9   0.0  1.1e-103  1.1e-103       1     361 [.       7     374 ..       7     375 .. 0.94

  Alignments for each domain:
  == domain 1  score: 332.9 bits;  conditional E-value: 1.1e-103
                           TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqy.kslieeheavrtkaGlfDvshmgkvels...Gs..kslkfLqrll 69 
                                         lk+tpL+ lh +lg+++v+faG+ +Pvqy +++ +eh  +r +aGlfDvshmg++ ++   G+  ++  +L++l+
  lcl|FitnessBrowser__Smeli:SMc02047   7 LKHTPLHALHLSLGARMVPFAGYDMPVQYpEGVLKEHLHTRAAAGLFDVSHMGQIVVRpksGKieDAALALEKLV 81 
                                         689**************************5588***********************972224322567789**** PP

                           TIGR00528  70 anDvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisll 144
                                         ++Dv  L++G+ +y  + na GG++DDl++ ++g+   + lvvnaa+++ Dl++lk+ l    ++  l+ + +l+
  lcl|FitnessBrowser__Smeli:SMc02047  82 PADVLGLAEGRQRYGLFTNAAGGILDDLMIVNRGDH--LFLVVNAACKDADLAHLKDGLGSVCDVTMLT-DRALI 153
                                         **********************************99..99*******************9999887665.579** PP

                           TIGR00528 145 alqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkP 219
                                         alqGP+a ++l +l  ++v++++ f+ v ea+l    ++i+r+GytGedGfei+++ e av++ ++l+e++ v P
  lcl|FitnessBrowser__Smeli:SMc02047 154 ALQGPRAGAVLCELW-ADVSSMR-FMDVTEADLHDVSCIISRSGYTGEDGFEISIPAEAAVDVTQRLLEHPDVLP 226
                                         *************97.6899996.77788****9999************************************** PP

                           TIGR00528 220 iGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkker.....kksdfiGravleeqkengtekklvGleml 289
                                         iGLgarD+Lrleag++LyG+++d +++P+eagl+w+++k+r     +   f G   +     +g+ +++vGl+  
  lcl|FitnessBrowser__Smeli:SMc02047 227 IGLGARDSLRLEAGLCLYGNDIDTNTSPIEAGLEWAIQKSRraggeRAGGFPGAGRILAELTDGVSRRRVGLRPE 301
                                         ****************************************9999888899************************* PP

                           TIGR00528 290 ekgiarnelkvllt.ngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                          +   r + +++   +g +  G vtsG + P ++  +a++yvd e +++Gt+l  evr+k ++i v+  +f++
  lcl|FitnessBrowser__Smeli:SMc02047 302 GRAPVRGNANLFADeEGRTAAGTVTSGGFGPSVDGPVAMGYVDAEHAEVGTRLFAEVRGKYLPIAVTALPFIK 374
                                         ***99*****99987999***************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (379 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.40
//
[ok]

This GapMind analysis is from Sep 17 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