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

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC 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.8961.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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.49
//
[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:

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis