GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcvT in Caulobacter crescentus NA1000

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate CCNA_03465 CCNA_03465 glycine cleavage system aminomethyltransferase T

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



>lcl|FitnessBrowser__Caulo:CCNA_03465 CCNA_03465 glycine cleavage
           system aminomethyltransferase T
          Length = 375

 Score =  369 bits (948), Expect = e-107
 Identities = 200/372 (53%), Positives = 242/372 (65%), Gaps = 5/372 (1%)

Query: 2   STEQLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIR 61
           S + L KTPL+  H+  GARMVPFAGY MPVQY  GV+KEH  TR+ AGLFDVSHMGQ R
Sbjct: 7   SDQDLKKTPLYDAHVAAGARMVPFAGYSMPVQYKDGVLKEHLWTREHAGLFDVSHMGQAR 66

Query: 62  LTGANAAKALETLVPVDIIDLPVGMQRYAMFTNATGGILDDLMVANLGNDELFLVVNAAC 121
           + G N AK+ E +V  D   L  G QRY +  NA GGI+DDLM A    D LF+VVN AC
Sbjct: 67  IRGENPAKSFEKVVSADYQGLKAGKQRYGVLLNADGGIVDDLMTARPDEDGLFVVVNGAC 126

Query: 122 KDQDLAHLRKHIGDQCTIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFARVKLL 181
           KD D A + + +  + T+  L E+RALLALQGP A  VLA   PE A+M FM    +   
Sbjct: 127 KDNDYAIIARELAGEATVTRL-EDRALLALQGPEAAAVLAAHVPEAAQMVFMDAKALSAF 185

Query: 182 GVDCFVSRSGYTGEDGFEISVPATNAEALARALLAEAEVAAIGLGARDSLRLEAGLCLYG 241
           GVD  +SRSGYTGEDG+EISVPA  AE +   LLA+  V  IGLGARDSLRLEAGL LYG
Sbjct: 186 GVDAIISRSGYTGEDGYEISVPADAAERVWNTLLADERVKPIGLGARDSLRLEAGLPLYG 245

Query: 242 HDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQAGVSRKRVGLLPQERTP 301
           HD++   +PIEA L +A+ + RR     AG + GA  +  +    +SR RV L   E  P
Sbjct: 246 HDLDETVSPIEAGLNFAVGRSRR----EAGDYLGAARIAKELAGELSRVRVNLKVLEGAP 301

Query: 302 VREGAEIVNEAGDIIGSVCSGGFGPTLGGPLAMGYVDSAYIALDTPVWAIVRGKKVPLLV 361
            REGAEI +EAG++IG V SGGF P+LG P+A+G+   AY A+ T +  IVRGK     V
Sbjct: 302 AREGAEIADEAGNVIGKVTSGGFAPSLGFPIAIGFAPPAYAAVGTKLKVIVRGKPAAAEV 361

Query: 362 SKMPFVPQRYYR 373
              PFVP RY R
Sbjct: 362 VASPFVPNRYVR 373


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: 420
Number of extensions: 19
Number of successful extensions: 3
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: 375
Length adjustment: 30
Effective length of query: 344
Effective length of database: 345
Effective search space:   118680
Effective search space used:   118680
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 CCNA_03465 CCNA_03465 (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.8326.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.7e-111  356.6   0.0   7.7e-111  356.4   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03465  CCNA_03465 glycine cleavage syst


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03465  CCNA_03465 glycine cleavage system aminomethyltransferase T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.4   0.0  7.7e-111  7.7e-111       1     361 [.      11     368 ..      11     369 .. 0.94

  Alignments for each domain:
  == domain 1  score: 356.4 bits;  conditional E-value: 7.7e-111
                             TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqyk.slieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanD 72 
                                           lk+tpLyd h+  g+++v+faG+++Pvqyk ++ +eh ++r++aGlfDvshmg+ +++G++  k +++++++D
  lcl|FitnessBrowser__Caulo:CCNA_03465  11 LKKTPLYDAHVAAGARMVPFAGYSMPVQYKdGVLKEHLWTREHAGLFDVSHMGQARIRGENPAKSFEKVVSAD 83 
                                           69***************************84679*************************************** PP

                             TIGR00528  73 vdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeislla 145
                                            + L  Gk +y vllna+GG+vDDl+  +  ed  + +vvn a+++ D + +  +l++e+t+  l  + +lla
  lcl|FitnessBrowser__Caulo:CCNA_03465  84 YQGLKAGKQRYGVLLNADGGIVDDLMTARPDED-GLFVVVNGACKDNDYAIIARELAGEATVTRLE-DRALLA 154
                                           **************************9999999.8999*********************9998775.679*** PP

                             TIGR00528 146 lqGPkaktiledlldkaveglkefffvqeaela..lkkaliartGytGedGfeiavanekavelwkklveayg 216
                                           lqGP+a+++l      +v++  +++f++++ l+  + +a+i+r+GytGedG+ei+v+ + a  +w++l+++  
  lcl|FitnessBrowser__Caulo:CCNA_03465 155 LQGPEAAAVLAA----HVPEAAQMVFMDAKALSafGVDAIISRSGYTGEDGYEISVPADAAERVWNTLLADER 223
                                           *********975....56666667777777765226799********************************** PP

                             TIGR00528 217 vkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkker.kksdfiGravleeqkengtekklvGlem 288
                                           vkPiGLgarD+Lrleag++LyG++lde+++P+eagl+++v ++r +  d++G a + +  + +  + +v l++
  lcl|FitnessBrowser__Caulo:CCNA_03465 224 VKPIGLGARDSLRLEAGLPLYGHDLDETVSPIEAGLNFAVGRSRrEAGDYLGAARIAKELAGELSRVRVNLKV 296
                                           ****************************************99984678************************* PP

                             TIGR00528 289 lekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                           le   ar++ ++   ++ + +G+vtsG ++P Lg  ia+++ +  ++ +Gtkl+v vr+k   ++vv  +fv+
  lcl|FitnessBrowser__Caulo:CCNA_03465 297 LEGAPAREGAEIAD-EAGNVIGKVTSGGFAPSLGFPIAIGFAPPAYAAVGTKLKVIVRGKPAAAEVVASPFVP 368
                                           **************.5559****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (375 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: 00:00:00.02
# Mc/sec: 6.53
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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