GapMind for Amino acid biosynthesis

 

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

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_011385559.1 AMB_RS16135 phosphoserine transaminase

Query= metacyc::MONOMER-15918
         (370 letters)



>NCBI__GCF_000009985.1:WP_011385559.1
          Length = 392

 Score =  497 bits (1279), Expect = e-145
 Identities = 235/379 (62%), Positives = 291/379 (76%), Gaps = 10/379 (2%)

Query: 2   KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61
           KP   P NP FSSGPCAK PG++V+ LKDTP GRSHR+K GK KL E I RTR +LG+P 
Sbjct: 6   KPAAKPANPNFSSGPCAKRPGWTVDALKDTPVGRSHRAKIGKTKLEELINRTRSVLGIPA 65

Query: 62  DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121
           DY +GIVPASDTGA EM +WS+LG RG+D L WESF +GW TDITKQLK++DTRVF+A Y
Sbjct: 66  DYRIGIVPASDTGAVEMAMWSLLGARGIDALAWESFGEGWVTDITKQLKIEDTRVFKAPY 125

Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181
           G LP+L +VD   DVVF WNGTT GV++PN DWI  DR+G+T+CDATSA+FAMD+P+ KL
Sbjct: 126 GTLPNLAEVDCDRDVVFTWNGTTGGVRIPNGDWIKSDRKGLTICDATSAVFAMDMPWDKL 185

Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241
           DV+T+SWQKVLGGEGAHGML+LSPRAV+RLE+Y P+WPLPKIFR+TKGGKL + IF G T
Sbjct: 186 DVVTWSWQKVLGGEGAHGMLVLSPRAVERLETYKPSWPLPKIFRMTKGGKLIEGIFKGET 245

Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301
           INTPSM+A ED +  LKWAES+GGLK LI R+  NL   ++++ K+ W   LA+  ++RS
Sbjct: 246 INTPSMIAVEDQIDALKWAESIGGLKALIARSEANLKAVQSWLDKSAWAANLADDAKVRS 305

Query: 302 STSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVE 351
            TS+C  V          D      K+++  L+KE VAYDIG+YRDAP+GLR+W GATVE
Sbjct: 306 CTSICMIVKAPFFAKLSPDDQAAAAKKIVTLLDKEGVAYDIGAYRDAPAGLRVWGGATVE 365

Query: 352 KEDLECLCEWIEWAYNLVK 370
             D+E L  W++WA+  VK
Sbjct: 366 TSDVEKLLPWLDWAFAQVK 384


Lambda     K      H
   0.319    0.136    0.430 

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: 545
Number of extensions: 22
Number of successful extensions: 2
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: 370
Length of database: 392
Length adjustment: 30
Effective length of query: 340
Effective length of database: 362
Effective search space:   123080
Effective search space used:   123080
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_011385559.1 AMB_RS16135 (phosphoserine transaminase)
to HMM TIGR01365 (phosphoserine aminotransferase (EC 2.6.1.52))

# 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.aa/TIGR01365.hmm
# target sequence database:        /tmp/gapView.8760.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01365  [M=374]
Accession:   TIGR01365
Description: serC_2: phosphoserine aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.4e-203  659.8   3.6   7.4e-203  659.6   3.6    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011385559.1  AMB_RS16135 phosphoserine transa


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011385559.1  AMB_RS16135 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  659.6   3.6  7.4e-203  7.4e-203       1     373 [.      10     382 ..      10     383 .. 0.99

  Alignments for each domain:
  == domain 1  score: 659.6 bits;  conditional E-value: 7.4e-203
                                 TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 
                                               +panp+fssgpcakrpg++v++lk++++grshr+k+gk+kl+e i++tr vl++pady+igiv+asdtg
  lcl|NCBI__GCF_000009985.1:WP_011385559.1  10 KPANPNFSSGPCAKRPGWTVDALKDTPVGRSHRAKIGKTKLEELINRTRSVLGIPADYRIGIVPASDTG 78 
                                               69******************************************************************* PP

                                 TIGR01365  70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138
                                               avema+wsllgarg+d la+esfg+gwvtd+tkqlk++d rv++a+yg lp+l+ vd ++dvvftwngt
  lcl|NCBI__GCF_000009985.1:WP_011385559.1  79 AVEMAMWSLLGARGIDALAWESFGEGWVTDITKQLKIEDTRVFKAPYGTLPNLAEVDCDRDVVFTWNGT 147
                                               ********************************************************************* PP

                                 TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207
                                               t gvr+pngd+i +dr+glticdatsa+fa+d++++kldvvt+swqkvlggegahg+l+lsprav+rle
  lcl|NCBI__GCF_000009985.1:WP_011385559.1 148 TGGVRIPNGDWIKSDRKGLTICDATSAVFAMDMPWDKLDVVTWSWQKVLGGEGAHGMLVLSPRAVERLE 216
                                               ********************************************************************* PP

                                 TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276
                                               +y+p+wplpkifr+tkggkl+++if+getintpsm+aved +dalkwaesigglkal+ar+++nl+ ++
  lcl|NCBI__GCF_000009985.1:WP_011385559.1 217 TYKPSWPLPKIFRMTKGGKLIEGIFKGETINTPSMIAVEDQIDALKWAESIGGLKALIARSEANLKAVQ 285
                                               ********************************************************************* PP

                                 TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345
                                               ++++ks+w   la   ++rs ts+c+ v  p  a l  d qa  ak++v++l+kegvaydig+yrdapa
  lcl|NCBI__GCF_000009985.1:WP_011385559.1 286 SWLDKSAWAANLADDAKVRSCTSICMIVKAPFFAKLSPDDQAAAAKKIVTLLDKEGVAYDIGAYRDAPA 354
                                               ***********************************99999***************************** PP

                                 TIGR01365 346 glriwcgatveksdleallewldwafal 373
                                               glr+w gatve+sd+e ll+wldwafa 
  lcl|NCBI__GCF_000009985.1:WP_011385559.1 355 GLRVWGGATVETSDVEKLLPWLDWAFAQ 382
                                               **************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (392 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.87
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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