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

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.32348.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.32
//
[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