GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Echinicola vietnamensis KMM 6221, DSM 17526

Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate Echvi_0091 Echvi_0091 glycine cleavage system T protein

Query= curated2:A6GXW3
         (360 letters)



>FitnessBrowser__Cola:Echvi_0091
          Length = 364

 Score =  486 bits (1252), Expect = e-142
 Identities = 234/360 (65%), Positives = 283/360 (78%)

Query: 1   MKNTALTNIHESLGAKMVPFAGYNMPVQYEGVNAEHEIVRTGVGVFDVSHMGEFFLKGEN 60
           +K  AL + H  LG KMVPFAGY+MPV+Y     EH  VR GVGVFDVSHMGEF + G +
Sbjct: 5   IKKIALNDKHIELGGKMVPFAGYHMPVRYSSDKEEHNTVRNGVGVFDVSHMGEFMVTGPH 64

Query: 61  ALALIQKVTSNDASKLVDGKAQYSCLPNNEGGIVDDLIIYKIADNHYMLVVNASNIEKDW 120
           ALALIQKVTSNDA+KLV G+AQYSCLPN  GGIVDDL++YK+ +  Y+LVVNASNIEKDW
Sbjct: 65  ALALIQKVTSNDAAKLVIGQAQYSCLPNETGGIVDDLLVYKMDEEKYLLVVNASNIEKDW 124

Query: 121 NWISSHNDLGVDMQNLSDSYSLLAIQGPKAAEAMQSLTSIDLVNMPYYSFQIGEFAGLKD 180
           NWI+ HND+G  ++N+SD  SL A+QGPKA E +Q +T ++L  + +Y F +GEFAG KD
Sbjct: 125 NWINQHNDMGAALENISDEMSLFAVQGPKAVETLQKVTPVNLDEVKFYHFTVGEFAGKKD 184

Query: 181 VTVSATGYTGSGGFEIYFKNEDAEAIWNKIFEAGKPFGIKPIGLAARDTLRLEMGFCLYG 240
           V +S TGYTG+GGFEIY KNEDA  +WN IFEAG+  GIKPIGL ARDTLR+EMG+CLYG
Sbjct: 185 VIISGTGYTGAGGFEIYVKNEDALDVWNAIFEAGEAAGIKPIGLGARDTLRMEMGYCLYG 244

Query: 241 NDINDTTSPLEAGLGWITKFDKEFTNSANLKKQKEEGVARKLVAFEMQERAVPRHDYEIV 300
           NDI+DTTSPLEAGLGWITKF K+F NS NLKKQKEEGV RKLV F+ +++ +PR  Y IV
Sbjct: 245 NDIDDTTSPLEAGLGWITKFTKDFINSENLKKQKEEGVTRKLVGFKFKDKGIPRAHYPIV 304

Query: 301 DASGNVIGIVTSGTMSPSMNIGIGLGYVPTSFSTVDSDIFIRIRKNDVLAKVVKLPFYKK 360
           + +G  IG VTSGTMSPSMNIGIGLGYV  +++   ++I I +R  ++ A V KLP  KK
Sbjct: 305 NEAGKQIGEVTSGTMSPSMNIGIGLGYVEKAYAKPGTEIAITVRNKNLAAVVEKLPLLKK 364


Lambda     K      H
   0.317    0.135    0.392 

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: 461
Number of extensions: 11
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: 360
Length of database: 364
Length adjustment: 29
Effective length of query: 331
Effective length of database: 335
Effective search space:   110885
Effective search space used:   110885
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate Echvi_0091 Echvi_0091 (glycine cleavage system T protein)
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.14949.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.1e-129  418.5   0.4   1.2e-129  418.3   0.4    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0091  Echvi_0091 glycine cleavage syst


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0091  Echvi_0091 glycine cleavage system T protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.3   0.4  1.2e-129  1.2e-129       2     361 ..       6     363 ..       5     364 .] 0.97

  Alignments for each domain:
  == domain 1  score: 418.3 bits;  conditional E-value: 1.2e-129
                            TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvda 75 
                                          k+ +L d h elggk+v+faG+++Pv+y+s +eeh+ vr+ +G+fDvshmg++ ++G+++l+++q++++nD ++
  lcl|FitnessBrowser__Cola:Echvi_0091   6 KKIALNDKHIELGGKMVPFAGYHMPVRYSSDKEEHNTVRNGVGVFDVSHMGEFMVTGPHALALIQKVTSNDAAK 79 
                                          899*********************************************************************** PP

                            TIGR00528  76 LtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP 149
                                          L  G+aqys l n  GG+vDDl+vyk  e+ ++llvvna+++ekD +w+++h + ++ l+++s+e+sl a+qGP
  lcl|FitnessBrowser__Cola:Echvi_0091  80 LVIGQAQYSCLPNETGGIVDDLLVYKMDEE-KYLLVVNASNIEKDWNWINQHNDMGAALENISDEMSLFAVQGP 152
                                          ***************************999.******************************************* PP

                            TIGR00528 150 kaktiledlldkaveglkefffvqeaelalkka.liartGytGedGfeiavanekavelwkklvea...ygvkP 219
                                          ka + l++++  +++++k + f   +e+a+kk  +i+ tGytG  Gfei+v+ne+a ++w+++ ea    g+kP
  lcl|FitnessBrowser__Cola:Echvi_0091 153 KAVETLQKVTPVNLDEVKFYHFT-VGEFAGKKDvIISGTGYTGAGGFEIYVKNEDALDVWNAIFEAgeaAGIKP 225
                                          *****************977776.99**99877589***************************9987779**** PP

                            TIGR00528 220 iGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgi 293
                                          iGLgarDtLr+e g +LyG+++d++++Pleaglgw+ k     +dfi  + l++qke+g+ +klvG+++ +kgi
  lcl|FitnessBrowser__Cola:Echvi_0091 226 IGLGARDTLRMEMGYCLYGNDIDDTTSPLEAGLGWITKFT---KDFINSENLKKQKEEGVTRKLVGFKFKDKGI 296
                                          ************************************9999...9****************************** PP

                            TIGR00528 294 arnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                          +r +++++  ++ k++G vtsGt+sP +++ i+l+yv+k ++k Gt++ + vrnk + + v k ++++
  lcl|FitnessBrowser__Cola:Echvi_0091 297 PRAHYPIVN-EAGKQIGEVTSGTMSPSMNIGIGLGYVEKAYAKPGTEIAITVRNKNLAAVVEKLPLLK 363
                                          *********.555**************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (364 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.32
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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