GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Pseudomonas fluorescens FW300-N2E3

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate AO353_03510 AO353_03510 glycine cleavage system protein T

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



>FitnessBrowser__pseudo3_N2E3:AO353_03510
          Length = 374

 Score =  717 bits (1851), Expect = 0.0
 Identities = 361/374 (96%), Positives = 366/374 (97%)

Query: 1   MSTEQLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60
           MSTEQLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI
Sbjct: 1   MSTEQLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60

Query: 61  RLTGANAAKALETLVPVDIIDLPVGMQRYAMFTNATGGILDDLMVANLGNDELFLVVNAA 120
           RLTGANAAKALETLVPVDIIDLPVGMQRYAMFTN  GGILDDLMVANLGNDELFLVVNAA
Sbjct: 61  RLTGANAAKALETLVPVDIIDLPVGMQRYAMFTNQNGGILDDLMVANLGNDELFLVVNAA 120

Query: 121 CKDQDLAHLRKHIGDQCTIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFARVKL 180
           CKDQDLAHLR+HIGDQC+IEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQF RV L
Sbjct: 121 CKDQDLAHLRQHIGDQCSIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFTRVTL 180

Query: 181 LGVDCFVSRSGYTGEDGFEISVPATNAEALARALLAEAEVAAIGLGARDSLRLEAGLCLY 240
           LGVDCFVSRSGYTGEDGFEISVPA +AEALARALLAE EVAAIGLGARDSLRLEAGLCLY
Sbjct: 181 LGVDCFVSRSGYTGEDGFEISVPAADAEALARALLAEPEVAAIGLGARDSLRLEAGLCLY 240

Query: 241 GHDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQAGVSRKRVGLLPQERT 300
           GHDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQ GVSRKRVGLLPQERT
Sbjct: 241 GHDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQNGVSRKRVGLLPQERT 300

Query: 301 PVREGAEIVNEAGDIIGSVCSGGFGPTLGGPLAMGYVDSAYIALDTPVWAIVRGKKVPLL 360
           PVREGAEIVNEAG+IIGSVCSGGFGPTLGGPLAMGY+DSAYIALDT VWAIVRGKKVPLL
Sbjct: 301 PVREGAEIVNEAGEIIGSVCSGGFGPTLGGPLAMGYLDSAYIALDTQVWAIVRGKKVPLL 360

Query: 361 VSKMPFVPQRYYRG 374
           VSKMPFVPQRYYRG
Sbjct: 361 VSKMPFVPQRYYRG 374


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: 626
Number of extensions: 21
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: 374
Length of database: 374
Length adjustment: 30
Effective length of query: 344
Effective length of database: 344
Effective search space:   118336
Effective search space used:   118336
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 AO353_03510 AO353_03510 (glycine cleavage system protein 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.5866.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   5.5e-111  356.9   0.0   6.3e-111  356.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510  AO353_03510 glycine cleavage sys


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510  AO353_03510 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.7   0.0  6.3e-111  6.3e-111       2     361 ..       7     368 ..       6     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 356.7 bits;  conditional E-value: 6.3e-111
                                     TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqyk.slieeheavrtkaGlfDvshmgkvelsGskslkfL 65 
                                                    +tpL+ lh elg+++v+faG+ +Pvqy  ++++eh+ +r++aGlfDvshmg+++l+G ++ k+L
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510   7 LKTPLHALHIELGARMVPFAGYDMPVQYPlGVMKEHQHTRDQAGLFDVSHMGQIRLTGANAAKAL 71 
                                                   79**************************6488********************************* PP

                                     TIGR00528  66 qrllanDvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehlee 130
                                                   + l++ D+  L++G  +y+ + n +GG++DDl+v + g+d ++ lvvnaa++++Dl++l++h+ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510  72 ETLVPVDIIDLPVGMQRYAMFTNQNGGILDDLMVANLGND-ELFLVVNAACKDQDLAHLRQHIGD 135
                                                   ****************************************.999********************* PP

                                     TIGR00528 131 evtldtlskeisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGf 195
                                                   + +++ l +e +llalqGP a t+l  l   +v ++  + f  +  l++ +++++r+GytGedGf
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 136 QCSIEPLFEERALLALQGPAAVTVLARLAP-EVAKMTFMQFT-RVTLLGVDCFVSRSGYTGEDGF 198
                                                   **************************9976.56677655555.88999***************** PP

                                     TIGR00528 196 eiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkker 260
                                                   ei+v+  +a  l+++l++++ v  iGLgarD+Lrleag++LyG++++ ++tP+ea+l w+++k r
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 199 EISVPAADAEALARALLAEPEVAAIGLGARDSLRLEAGLCLYGHDMNTDTTPIEASLLWAISKPR 263
                                                   ***************************************************************99 PP

                                     TIGR00528 261 .....kksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPt 320
                                                        +   f G +++  q++ng+ +k+vGl   e+   r++ +++  ++ +++G v sG + Pt
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 264 radgaRAGGFPGAETVFAQQQNGVSRKRVGLLPQERTPVREGAEIVN-EAGEIIGSVCSGGFGPT 327
                                                   888877889**************************************.555************** PP

                                     TIGR00528 321 LgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                                   Lg  +a++y+d+ +    t++   vr+k+v++ v k++fv+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03510 328 LGGPLAMGYLDSAYIALDTQVWAIVRGKKVPLLVSKMPFVP 368
                                                   ***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (374 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: 9.15
//
[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