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.11693.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.19
//
[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:

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