Alignments for a candidate for gcvT in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Magnetospirillum magneticum AMB-1

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate WP_011383209.1 AMB_RS03925 glycine cleavage system protein T

Query= reanno::WCS417:GFF4369
         (374 letters)



>NCBI__GCF_000009985.1:WP_011383209.1
          Length = 371

 Score =  417 bits (1072), Expect = e-121
 Identities = 208/373 (55%), Positives = 261/373 (69%), Gaps = 5/373 (1%)

Query: 2   STETLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHLHTRDQAGLFDVSHMGQIR 61
           S   +L  PL ALH ELGA+MVPFAGY MPVQYP GV+ EHLHTR  A LFDVSHMGQ  
Sbjct: 4   SETPMLTVPLDALHRELGAKMVPFAGYSMPVQYPAGVLAEHLHTRSGAALFDVSHMGQAS 63

Query: 62  LTGANAAKALETLVPVDILDLPVGMQRYAMFTNDQGGILDDLMVANLGNEELFLVVNAAC 121
           + GA A + LETLVP DI  L +G  RY++FTNDQGGILDDLM++ L  + LFLV+NAAC
Sbjct: 64  IRGAKAVELLETLVPGDIQALGLGKTRYSVFTNDQGGILDDLMISKLAEDHLFLVINAAC 123

Query: 122 KDQDLAHLRQHIGDQCTIEPLFEERALLALQGPAAVKVLARLAPEVTKMTFMQFATLRLL 181
           K  D AHL+ H+GD+  +  + E+R+LLALQGP A   +  L PE   MTFM  A + + 
Sbjct: 124 KHADFAHLKAHLGDKVELS-MIEDRSLLALQGPGAAAAMVTLCPEAGAMTFMTIAEITVA 182

Query: 182 GVDCYVSRSGYTGEDGFEISVPAANAESLARSLLAETEVQAIGLGARDSLRLEAGLCLYG 241
           G+ C  +RSGYTGEDG+EISV  A+ E+LAR++LA   V   GLGARDSLRLEAGLCLYG
Sbjct: 183 GIKCLATRSGYTGEDGWEISVANADVETLARAILAAPGVMPAGLGARDSLRLEAGLCLYG 242

Query: 242 HDMNTDTTPIEASLLWAISKARRADGARAGGFPGADTIFTQQQAGVSRKRVGLLPQERTP 301
            D++T TTP+EAS+ W +SK RRA+    GGFPGA  I  Q   G  R+RVG+ P  + P
Sbjct: 243 SDIDTTTTPVEASIAWIMSKRRRAE----GGFPGAAVIQKQLAEGAPRRRVGIQPDGKAP 298

Query: 302 VREGAQIVDADGTVIGSVCSGGFGSTLGGPLAMGYLDSAFIALDTEVSALVRGKKVPLRV 361
            R   +I D  G  +G +CSGGFG + GGP+AMGY+ +AF  + T++  +VRGK +   V
Sbjct: 299 ARAHTEITDEAGNRLGEICSGGFGPSAGGPVAMGYVPAAFAGVGTKLKLVVRGKAMDAHV 358

Query: 362 SKMPFVPQRYYRG 374
             +PFVP RY++G
Sbjct: 359 CDLPFVPHRYFKG 371


Lambda     K      H
   0.321    0.137    0.398 

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: 459
Number of extensions: 16
Number of successful extensions: 3
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: 374
Length of database: 371
Length adjustment: 30
Effective length of query: 344
Effective length of database: 341
Effective search space:   117304
Effective search space used:   117304
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: 50 (23.9 bits)

Align candidate WP_011383209.1 AMB_RS03925 (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.17278.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-103  332.2   0.0     2e-103  332.0   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383209.1  AMB_RS03925 glycine cleavage sys


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383209.1  AMB_RS03925 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.0   0.0    2e-103    2e-103       4     361 ..      11     365 ..       8     366 .. 0.95

  Alignments for each domain:
  == domain 1  score: 332.0 bits;  conditional E-value: 2e-103
                                 TIGR00528   4 tpLydlhtelggklvdfaGwelPvqy.kslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllan 71 
                                                pL  lh elg+k+v+faG+++Pvqy +++  eh  +r  a lfDvshmg+ +++G k++++L+ l++ 
  lcl|NCBI__GCF_000009985.1:WP_011383209.1  11 VPLDALHRELGAKMVPFAGYSMPVQYpAGVLAEHLHTRSGAALFDVSHMGQASIRGAKAVELLETLVPG 79 
                                               58899*********************55779************************************** PP

                                 TIGR00528  72 DvdaLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlske 140
                                               D++aL  Gk++ysv+ n qGG++DDl++ k +ed ++ lv+naa+++ D ++lk hl ++v+l  + ++
  lcl|NCBI__GCF_000009985.1:WP_011383209.1  80 DIQALGLGKTRYSVFTNDQGGILDDLMISKLAED-HLFLVINAACKHADFAHLKAHLGDKVELSMI-ED 146
                                               **********************************.999**********************999765.66 PP

                                 TIGR00528 141 isllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwk 209
                                                sllalqGP a++ +  l  +a +++  f+ + e  +a+ k+l +r+GytGedG+ei+van +   l++
  lcl|NCBI__GCF_000009985.1:WP_011383209.1 147 RSLLALQGPGAAAAMVTLCPEA-GAM-TFMTIAEITVAGIKCLATRSGYTGEDGWEISVANADVETLAR 213
                                               89********999999888654.444.6778888899999***************************** PP

                                 TIGR00528 210 klveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkker.kksdfiGravleeqken 277
                                               ++++a+gv P GLgarD+Lrleag++LyG ++d ++tP+ea++ w+++k r ++  f G av+++q ++
  lcl|NCBI__GCF_000009985.1:WP_011383209.1 214 AILAAPGVMPAGLGARDSLRLEAGLCLYGSDIDTTTTPVEASIAWIMSKRRrAEGGFPGAAVIQKQLAE 282
                                               ***********************************************99875899************** PP

                                 TIGR00528 278 gtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevr 346
                                               g+ +++vG++   k  ar + ++   ++ ++ G + sG + P  g  +a++yv+  ++++Gtkl+  vr
  lcl|NCBI__GCF_000009985.1:WP_011383209.1 283 GAPRRRVGIQPDGKAPARAHTEITD-EAGNRLGEICSGGFGPSAGGPVAMGYVPAAFAGVGTKLKLVVR 350
                                               *************************.55599************************************** PP

                                 TIGR00528 347 nklvkikvvkklfvr 361
                                               +k ++++v   +fv+
  lcl|NCBI__GCF_000009985.1:WP_011383209.1 351 GKAMDAHVCDLPFVP 365
                                               ***********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (371 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: 7.43
//
[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