Alignments for a candidate for gcvT in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Paraburkholderia bryophila 376MFSha3.1

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate H281DRAFT_02411 H281DRAFT_02411 aminomethyltransferase

Query= reanno::Koxy:BWI76_RS23880
         (364 letters)



>FitnessBrowser__Burk376:H281DRAFT_02411
          Length = 372

 Score =  358 bits (919), Expect = e-103
 Identities = 193/369 (52%), Positives = 244/369 (66%), Gaps = 12/369 (3%)

Query: 3   QQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGSRI 62
           + TPL   H    ARMVDF GW MP++YGSQIDEH AVR DAGMFDVSHM ++DF G R+
Sbjct: 5   KHTPLNATHRALNARMVDFGGWDMPVNYGSQIDEHRAVRTDAGMFDVSHMCVIDFTGERV 64

Query: 63  REFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREKDL 122
           R F  + LAN+VAKL  PG+ALYS +L A GGVIDDLIVY+  ED+FR+VVN+ T +KD+
Sbjct: 65  RGFFEHALANNVAKLQTPGRALYSCLLNADGGVIDDLIVYYFGEDHFRVVVNAGTADKDI 124

Query: 123 AWIAQQSE-SYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQA-- 179
           AW  Q +E  +GL IT R DL+++AVQGP A+EK       A R A E +KPF   +   
Sbjct: 125 AWFKQLNEGGFGLTITPRRDLAIVAVQGPNAREKVWQT-VPAIRSATETLKPFNAARVES 183

Query: 180 ---GDLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLY 236
              G+L +A TGYTGE G+EI +P +  V  W  L   GV+P GLGARDTLRLEAGMNLY
Sbjct: 184 TPFGELTVARTGYTGEDGFEIIVPADHVVALWNALQAQGVRPAGLGARDTLRLEAGMNLY 243

Query: 237 GQEMDEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGL 296
           GQ+MD+ +SPL A + WT+    + RDF+GR  LE    +     VGL++ ++     G+
Sbjct: 244 GQDMDDNISPLDAGLAWTVDL-TSARDFVGRSRLESDGSRAA--FVGLILLKENGKAAGV 300

Query: 297 PVRFSDADGNQKEGIITSGTFSPTLGYSIALARVPEGI--GETAVVQIRNREMPVKVTKP 354
                       EG ITSGTFSPT+  SIA ARVP+G+  G+T  VQIR++ +P  V K 
Sbjct: 301 LRAHQKVVTPHGEGEITSGTFSPTMQESIAFARVPKGVQPGDTVHVQIRDKSVPASVVKL 360

Query: 355 VFVRNGKAV 363
            FVRNGK +
Sbjct: 361 PFVRNGKVL 369


Lambda     K      H
   0.320    0.137    0.407 

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: 443
Number of extensions: 24
Number of successful extensions: 5
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: 364
Length of database: 372
Length adjustment: 30
Effective length of query: 334
Effective length of database: 342
Effective search space:   114228
Effective search space used:   114228
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: 49 (23.5 bits)

Align candidate H281DRAFT_02411 H281DRAFT_02411 (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.5643.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     2e-121  391.3   0.0   2.2e-121  391.1   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02411  H281DRAFT_02411 aminomethyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02411  H281DRAFT_02411 aminomethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  391.1   0.0  2.2e-121  2.2e-121       1     362 []       4     365 ..       4     365 .. 0.92

  Alignments for each domain:
  == domain 1  score: 391.1 bits;  conditional E-value: 2.2e-121
                                    TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLq 66 
                                                  lk+tpL   h  l +++vdf+Gw +Pv+y+s+i+eh+avrt+aG+fDvshm  ++ +G++++ f++
  lcl|FitnessBrowser__Burk376:H281DRAFT_02411   4 LKHTPLNATHRALNARMVDFGGWDMPVNYGSQIDEHRAVRTDAGMFDVSHMCVIDFTGERVRGFFE 69 
                                                  689*************************************************************** PP

                                    TIGR00528  67 rllanDvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleee 131
                                                  + lan+v++L + G+a+ys llna+GGv+DDlivy++ged +f++vvna+ta+kD +w+k+  e++
  lcl|FitnessBrowser__Burk376:H281DRAFT_02411  70 HALANNVAKLQTpGRALYSCLLNADGGVIDDLIVYYFGED-HFRVVVNAGTADKDIAWFKQLNEGG 134
                                                  **********655***************************.********************88876 PP

                                    TIGR00528 132 .vtldtlskeisllalqGPkakt.ile..dlldkaveglkefffvqeaelalkkaliartGytGed 193
                                                   +  +t +++++++a+qGP+a++ + +  ++++ a e lk+f     +     +  +artGytGed
  lcl|FitnessBrowser__Burk376:H281DRAFT_02411 135 fGLTITPRRDLAIVAVQGPNAREkVWQtvPAIRSATETLKPFNAARVESTPFGELTVARTGYTGED 200
                                                  155678899**********9965266633678999999****9987777777888*********** PP

                                    TIGR00528 194 GfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkke 259
                                                  Gfei+v+ ++ v lw++l ++ gv+P GLgarDtLrleagm+LyGq++d++i+Pl+agl w+v + 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02411 201 GFEIIVPADHVVALWNALQAQ-GVRPAGLGARDTLRLEAGMNLYGQDMDDNISPLDAGLAWTVDLT 265
                                                  ******************999.******************************************** PP

                                    TIGR00528 260 rkksdfiGravleeqkengtekklvGlemle...k..giarnelkvlltngekevGivtsGtlsPt 320
                                                   + +df+Gr+ le     g++   vGl +l+   k  g++r + kv++++g   +G +tsGt+sPt
  lcl|FitnessBrowser__Burk376:H281DRAFT_02411 266 -SARDFVGRSRLESD---GSRAAFVGLILLKengKaaGVLRAHQKVVTPHG---EGEITSGTFSPT 324
                                                  .9**********975...555556777776522243359*********999...9*********** PP

                                    TIGR00528 321 LgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                                  ++ +ia a+v+k++ + G++++v++r+k v++ vvk +fvr+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02411 325 MQESIAFARVPKGV-QPGDTVHVQIRDKSVPASVVKLPFVRN 365
                                                  ***********887.57***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (372 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: 10.78
//
[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