Alignments for a candidate for gcvT in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Pedobacter sp. GW460-11-11-14-LB5

Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate CA265_RS23960 CA265_RS23960 glycine cleavage system protein T

Query= curated2:A6GXW3
         (360 letters)



>FitnessBrowser__Pedo557:CA265_RS23960
          Length = 359

 Score =  518 bits (1335), Expect = e-152
 Identities = 248/359 (69%), Positives = 291/359 (81%)

Query: 1   MKNTALTNIHESLGAKMVPFAGYNMPVQYEGVNAEHEIVRTGVGVFDVSHMGEFFLKGEN 60
           MKNTALT  H +LGAKMVPFAGYNMPV YEG+NAEH  VR GVGVFDVSHMGEF LKGEN
Sbjct: 1   MKNTALTEKHIALGAKMVPFAGYNMPVTYEGINAEHATVRNGVGVFDVSHMGEFILKGEN 60

Query: 61  ALALIQKVTSNDASKLVDGKAQYSCLPNNEGGIVDDLIIYKIADNHYMLVVNASNIEKDW 120
           AL LIQ+VTSNDA+KL DGK QYSCLPN +GGIVDDL++YKI D  YMLVVNASNIEKDW
Sbjct: 61  ALDLIQRVTSNDAAKLYDGKVQYSCLPNKDGGIVDDLLVYKIDDKTYMLVVNASNIEKDW 120

Query: 121 NWISSHNDLGVDMQNLSDSYSLLAIQGPKAAEAMQSLTSIDLVNMPYYSFQIGEFAGLKD 180
           NWI   N   V+M N+SD  SLLAIQGPKAA+A+Q+LT +DL +M YY+F  G FAG+ +
Sbjct: 121 NWIQQFNSKDVEMHNISDQTSLLAIQGPKAADALQTLTDVDLASMEYYTFVKGTFAGVDN 180

Query: 181 VTVSATGYTGSGGFEIYFKNEDAEAIWNKIFEAGKPFGIKPIGLAARDTLRLEMGFCLYG 240
           V +SATGYTG+GGFEIYF+N+ A+ IW+ IF+AG P+ I+PIGL ARDTLRLEMGFCLYG
Sbjct: 181 VVISATGYTGAGGFEIYFENQYADQIWDAIFKAGAPYNIQPIGLGARDTLRLEMGFCLYG 240

Query: 241 NDINDTTSPLEAGLGWITKFDKEFTNSANLKKQKEEGVARKLVAFEMQERAVPRHDYEIV 300
           NDI+D+TSP+EAGLGWITKF K FTNS  L  QKE G+ +KLV FEM +R +PRHDYEI 
Sbjct: 241 NDIDDSTSPIEAGLGWITKFSKSFTNSEALLAQKEAGIQKKLVGFEMIDRGIPRHDYEIA 300

Query: 301 DASGNVIGIVTSGTMSPSMNIGIGLGYVPTSFSTVDSDIFIRIRKNDVLAKVVKLPFYK 359
           DA GN+IG VTSGT +PS+   IG+GY+   F+   +++FI IR   + AKVVK PFYK
Sbjct: 301 DAEGNIIGKVTSGTQAPSLQKAIGMGYIAKDFTKEGTEVFILIRNTPIKAKVVKFPFYK 359


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: 454
Number of extensions: 9
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: 359
Length adjustment: 29
Effective length of query: 331
Effective length of database: 330
Effective search space:   109230
Effective search space used:   109230
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 CA265_RS23960 CA265_RS23960 (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.15837.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.8e-127  410.5   0.3   3.1e-127  410.4   0.3    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS23960  CA265_RS23960 glycine cleavage s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS23960  CA265_RS23960 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.4   0.3  3.1e-127  3.1e-127       2     361 ..       2     359 .]       1     359 [] 0.98

  Alignments for each domain:
  == domain 1  score: 410.4 bits;  conditional E-value: 3.1e-127
                                  TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrll 69 
                                                k+t+L + h  lg+k+v+faG+++Pv y+++  eh  vr+ +G+fDvshmg++ l+G+++l+++qr++
  lcl|FitnessBrowser__Pedo557:CA265_RS23960   2 KNTALTEKHIALGAKMVPFAGYNMPVTYEGINAEHATVRNGVGVFDVSHMGEFILKGENALDLIQRVT 69 
                                                89****************************************************************** PP

                                  TIGR00528  70 anDvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtl 137
                                                +nD ++L  Gk qys l n +GG+vDDl+vyk  +  +++lvvna+++ekD +w+++  +++v+++++
  lcl|FitnessBrowser__Pedo557:CA265_RS23960  70 SNDAAKLYDGKVQYSCLPNKDGGIVDDLLVYKIDDK-TYMLVVNASNIEKDWNWIQQFNSKDVEMHNI 136
                                                *******************************98877.******************************* PP

                                  TIGR00528 138 skeisllalqGPkaktiledlldkaveglkefffvqeaelalkka.liartGytGedGfeiavaneka 204
                                                s++ slla+qGPka++ l+ l+d ++ +++ ++fv ++ +a+ +  +i+ tGytG  Gfei+ +n+ a
  lcl|FitnessBrowser__Pedo557:CA265_RS23960 137 SDQTSLLAIQGPKAADALQTLTDVDLASMEYYTFV-KGTFAGVDNvVISATGYTGAGGFEIYFENQYA 203
                                                ***********************************.88898877769********************* PP

                                  TIGR00528 205 velwkklvea...ygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGra 269
                                                 ++w ++ +a   y ++PiGLgarDtLrle g +LyG+++d++++P+eaglgw+ k +   + f   +
  lcl|FitnessBrowser__Pedo557:CA265_RS23960 204 DQIWDAIFKAgapYNIQPIGLGARDTLRLEMGFCLYGNDIDDSTSPIEAGLGWITKFS---KSFTNSE 268
                                                ********999999*****************************************999...88***** PP

                                  TIGR00528 270 vleeqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkeleki 337
                                                +l  qke g++kklvG+em+++gi+r+++++  ++g +++G+vtsGt++P L+k+i+++y+ k+++k 
  lcl|FitnessBrowser__Pedo557:CA265_RS23960 269 ALLAQKEAGIQKKLVGFEMIDRGIPRHDYEIADAEG-NIIGKVTSGTQAPSLQKAIGMGYIAKDFTKE 335
                                                *********************************999.9****************************** PP

                                  TIGR00528 338 Gtklevevrnklvkikvvkklfvr 361
                                                Gt++ + +rn  +k+kvvk +f++
  lcl|FitnessBrowser__Pedo557:CA265_RS23960 336 GTEVFILIRNTPIKAKVVKFPFYK 359
                                                **********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (359 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: 7.57
//
[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