Alignments for a candidate for gcvT in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Pseudomonas fluorescens FW300-N2E2

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate Pf6N2E2_5556 Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5556
         (374 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5556
          Length = 374

 Score =  743 bits (1917), Expect = 0.0
 Identities = 374/374 (100%), Positives = 374/374 (100%)

Query: 1   MSTEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60
           MSTEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI
Sbjct: 1   MSTEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60

Query: 61  RLTGAGAAKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLGNDELFLVVNAA 120
           RLTGAGAAKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLGNDELFLVVNAA
Sbjct: 61  RLTGAGAAKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLGNDELFLVVNAA 120

Query: 121 CKDQDLAHLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTL 180
           CKDQDLAHLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTL
Sbjct: 121 CKDQDLAHLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTL 180

Query: 181 LGMDCYVSRSGYTGEDGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLY 240
           LGMDCYVSRSGYTGEDGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLY
Sbjct: 181 LGMDCYVSRSGYTGEDGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLY 240

Query: 241 GHDMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQQQGGVKRKRVGLLPQERT 300
           GHDMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQQQGGVKRKRVGLLPQERT
Sbjct: 241 GHDMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQQQGGVKRKRVGLLPQERT 300

Query: 301 PVREGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGKKVPLL 360
           PVREGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGKKVPLL
Sbjct: 301 PVREGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGKKVPLL 360

Query: 361 VSKMPFVPQRYYRG 374
           VSKMPFVPQRYYRG
Sbjct: 361 VSKMPFVPQRYYRG 374


Lambda     K      H
   0.321    0.138    0.406 

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: 690
Number of extensions: 26
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 Pf6N2E2_5556 (Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10))
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.1214.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.1e-108  348.4   0.0   2.4e-108  348.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5556  Aminomethyltransferase (glycine 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5556  Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.2   0.0  2.4e-108  2.4e-108       2     361 ..       7     368 ..       6     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 348.2 bits;  conditional E-value: 2.4e-108
                                      TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqyk.slieeheavrtkaGlfDvshmgkvelsGskslkf 64 
                                                     +tpL+ lh elg+++v+faG+ +Pvqy  ++++eh+ +r++aGlfDvshmg+++l+G  + k+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5556   7 LKTPLHALHLELGARMVPFAGYDMPVQYPlGVMKEHQHTRDQAGLFDVSHMGQIRLTGAGAAKA 70 
                                                    79**************************6488******************************** PP

                                      TIGR00528  65 LqrllanDvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehl 128
                                                    L+ l++ D+  L++G  +y+ + n +GG++DDl+v + g+d ++ lvvnaa++++Dl++l+ h+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5556  71 LETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLGND-ELFLVVNAACKDQDLAHLRAHI 133
                                                    *****************************************.999******************* PP

                                      TIGR00528 129 eeevtldtlskeisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGe 192
                                                      + +++ l +  +llalqGP a t+l  l   +v ++  f+  q+  l++ +++++r+GytGe
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5556 134 GAQCSIEPLFEARALLALQGPAAVTVLARLAP-DVAKM-TFMQFQRVTLLGMDCYVSRSGYTGE 195
                                                    ***************************99875.66676.57777899***************** PP

                                      TIGR00528 193 dGfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvv 256
                                                    dGfei+v+  +a +l+++l++++ v  iGLgarD+Lrleag++LyG++++ e+tP+ea+l w++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5556 196 DGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLYGHDMNTETTPIEASLLWAI 259
                                                    **************************************************************** PP

                                      TIGR00528 257 kker.....kksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngekevGivtsG 315
                                                    +k r     +   f G +++  q++ g+++k+vGl   e+   r++ +++  ++ +++G v sG
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5556 260 SKVRradgaRAGGFPGAETVFAQQQGGVKRKRVGLLPQERTPVREGAEIVN-EAGEIIGTVCSG 322
                                                    *998888877889**************************************.555********* PP

                                      TIGR00528 316 tlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                                     + PtLg  +a++y+d+ +    t +   vr+k+v++ v k++fv+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5556 323 GFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGKKVPLLVSKMPFVP 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.63
//
[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