Alignments for a candidate for gcvT in Sinorhizobium meliloti 1021

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.1835499.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.30
//
[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:

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

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 catabolism of small carbon sources