Alignments for a candidate for gcvT in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Pseudomonas putida KT2440

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate PP_0986 PP_0986 aminomethyltransferase

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



>FitnessBrowser__Putida:PP_0986
          Length = 373

 Score =  602 bits (1553), Expect = e-177
 Identities = 300/372 (80%), Positives = 330/372 (88%)

Query: 3   TEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIRL 62
           +E LLKTPLHALHLELGARMVPFAGYDMPVQYPLGV+KEH HTR+QAGLFDVSHMGQI L
Sbjct: 2   SETLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVLKEHLHTREQAGLFDVSHMGQIIL 61

Query: 63  TGAGAAKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLGNDELFLVVNAACK 122
            GA AAKALE+LVPVDIIDLPVGMQRYAMFTNE GGILDDLMVANLG D LFLVVNAACK
Sbjct: 62  RGADAAKALESLVPVDIIDLPVGMQRYAMFTNEQGGILDDLMVANLGEDTLFLVVNAACK 121

Query: 123 DQDLAHLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTLLG 182
           +QDLAHL+ HIG++C ++PLFE RALLALQGPAAV VL RLAP+VA MTFMQF+RV LLG
Sbjct: 122 EQDLAHLQTHIGSRCEVQPLFEERALLALQGPAAVKVLERLAPEVAGMTFMQFRRVKLLG 181

Query: 183 MDCYVSRSGYTGEDGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLYGH 242
           +DC+VSRSGYTGEDG+EISVP   A+ LAR L+AEPEV  IGLGARDSLRLEAGLCLYGH
Sbjct: 182 VDCFVSRSGYTGEDGYEISVPVNAADALARRLMAEPEVQPIGLGARDSLRLEAGLCLYGH 241

Query: 243 DMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQQQGGVKRKRVGLLPQERTPV 302
           DMN+ETTPIEASLLWAISKVRRADGARA GFPGAE +FA  + GV RKRVGLLPQERTPV
Sbjct: 242 DMNSETTPIEASLLWAISKVRRADGARAAGFPGAEAIFAHVRDGVARKRVGLLPQERTPV 301

Query: 303 REGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGKKVPLLVS 362
           REGA+IV+   + +G VCSGGFGPTL  P+AMGY+DS + ALDT ++A+VRGKKV L VS
Sbjct: 302 REGADIVDANDKPVGKVCSGGFGPTLAAPVAMGYIDSEHAALDTALFAVVRGKKVALKVS 361

Query: 363 KMPFVPQRYYRG 374
           KMPFV  RYYRG
Sbjct: 362 KMPFVTPRYYRG 373


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: 589
Number of extensions: 22
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: 373
Length adjustment: 30
Effective length of query: 344
Effective length of database: 343
Effective search space:   117992
Effective search space used:   117992
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 PP_0986 PP_0986 (aminomethyltransferase)
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.32023.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.2e-111  356.5   0.0   8.4e-111  356.3   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0986  PP_0986 aminomethyltransferase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0986  PP_0986 aminomethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.3   0.0  8.4e-111  8.4e-111       2     360 ..       6     366 ..       5     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 356.3 bits;  conditional E-value: 8.4e-111
                           TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqyk.slieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvda 75 
                                          +tpL+ lh elg+++v+faG+ +Pvqy  ++ +eh  +r++aGlfDvshmg++ l+G ++ k+L++l++ D+  
  lcl|FitnessBrowser__Putida:PP_0986   6 LKTPLHALHLELGARMVPFAGYDMPVQYPlGVLKEHLHTREQAGLFDVSHMGQIILRGADAAKALESLVPVDIID 80 
                                         79**************************6488******************************************* PP

                           TIGR00528  76 LtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPk 150
                                         L++G  +y+ + n qGG++DDl+v + ged ++ lvvnaa++e+Dl++l+ h+    +++ l +e +llalqGP 
  lcl|FitnessBrowser__Putida:PP_0986  81 LPVGMQRYAMFTNEQGGILDDLMVANLGED-TLFLVVNAACKEQDLAHLQTHIGSRCEVQPLFEERALLALQGPA 154
                                         ******************************.999***************************************** PP

                           TIGR00528 151 aktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgar 225
                                         a ++le l   +v g+  + f  +  l++ +++++r+GytGedG+ei+v+ + a  l+++l++++ v+PiGLgar
  lcl|FitnessBrowser__Putida:PP_0986 155 AVKVLERLAP-EVAGMTFMQF-RRVKLLGVDCFVSRSGYTGEDGYEISVPVNAADALARRLMAEPEVQPIGLGAR 227
                                         ******9975.6788875555.5999************************************************* PP

                           TIGR00528 226 DtLrleagmaLyGqeldeeitPleaglgwvvkker.....kksdfiGravleeqkengtekklvGlemlekgiar 295
                                         D+Lrleag++LyG++++ e+tP+ea+l w+++k r     +   f G +++     +g+ +k+vGl   e+   r
  lcl|FitnessBrowser__Putida:PP_0986 228 DSLRLEAGLCLYGHDMNSETTPIEASLLWAISKVRradgaRAAGFPGAEAIFAHVRDGVARKRVGLLPQERTPVR 302
                                         ********************************998888877889******************************* PP

                           TIGR00528 296 nelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfv 360
                                         ++ +++ +n  k vG+v sG + PtL   +a++y+d+e +   t l   vr+k+v +kv k++fv
  lcl|FitnessBrowser__Putida:PP_0986 303 EGADIVDAND-KPVGKVCSGGFGPTLAAPVAMGYIDSEHAALDTALFAVVRGKKVALKVSKMPFV 366
                                         *******776.9****************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (373 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: 9.52
//
[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