Alignments for a candidate for serA in Desulfuromusa kysingii DSM 7343

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Desulfuromusa kysingii DSM 7343

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_092350915.1 BLU87_RS16615 phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>NCBI__GCF_900107645.1:WP_092350915.1
          Length = 531

 Score =  401 bits (1030), Expect = e-116
 Identities = 207/529 (39%), Positives = 330/529 (62%), Gaps = 9/529 (1%)

Query: 3   RVLVSDKMSNDGLQPLIESDFIEIVQKNVADAEDELHT----FDALLVRSATKVTEDLFN 58
           +VL++D++S++GL PL E   I I  K +  +  ELH     ++A++ RS T V + L +
Sbjct: 2   KVLITDEISDNGLLPLTEDPRIHI-DKKLGLSIPELHKIIGGYEAIITRSGTLVDKALLD 60

Query: 59  KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118
              +LKIV RAGVG+DN+D+D A+  G+IV+NAP GN  S AEHT A++ SL R++P AN
Sbjct: 61  CADNLKIVARAGVGIDNVDVDAASSKGIIVVNAPYGNVNSAAEHTMAIMLSLFRNVPMAN 120

Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKK 178
            S+K  +W R  + G EL GKT+GI+GLG++G  +A+R  AF   V  +DP+++E+RA  
Sbjct: 121 TSLKGGDWKRALFTGCELKGKTVGIIGLGKVGGRVARRCRAFEAEVITYDPYISEKRADD 180

Query: 179 IGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238
            GV  +  E+++  +D+ITVHTPL  ET+ +++ ++    K GV +INCARGGII+EAA+
Sbjct: 181 FGVKLQPLEDIIRFSDVITVHTPLNDETRNIISSDSFKGMKDGVVIINCARGGIINEAAM 240

Query: 239 LEALENGHVAGAALDVFEVEPP---VDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEE 295
           LEALE+G  AGAA DV+  EPP   V  KL+ HP ++ TPHLGA+T EAQ NVA  VS+E
Sbjct: 241 LEALESGKCAGAAFDVWSQEPPKTDVLQKLIAHPKMLVTPHLGANTFEAQKNVAVDVSKE 300

Query: 296 VLQFAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTI 355
           ++ +  G P+ +A+N+P    D+   +KP+ Q+   +G  +SQ        V   Y G +
Sbjct: 301 IVNYVDGRPLENAVNIPRFDPDQMEHMKPFMQLVSILGDFISQLAPPNPNKVTFTYNGQL 360

Query: 356 AKLETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKV 415
           A+ + + ++ + L+  L    D  VN VNA  +A+E GI      S+    + + I++ +
Sbjct: 361 ARFDCAPLSVSGLAALLNHCTDQEVNMVNASLIAREMGIEVESIRSTETDSFSSLITLSL 420

Query: 416 TGDRSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDND 475
              +   T+  T       +IV++  + IDF P   ++ I +QD +G+IG++G +LG+ D
Sbjct: 421 ESAQGRRTIAGTLF-EGTPKIVKMRDYAIDFRPEKDMLVINYQDRSGLIGKIGTVLGEAD 479

Query: 476 INIATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLIDL 524
           +NI  M +GR+EK GEA+++ S D  ++++ +++++       +K + L
Sbjct: 480 VNIGNMSLGRQEKAGEAMVVFSVDSPVDEETLQKVSEAVSPKFIKAVHL 528


Lambda     K      H
   0.317    0.134    0.374 

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: 648
Number of extensions: 20
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: 525
Length of database: 531
Length adjustment: 35
Effective length of query: 490
Effective length of database: 496
Effective search space:   243040
Effective search space used:   243040
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: 52 (24.6 bits)

Align candidate WP_092350915.1 BLU87_RS16615 (phosphoglycerate dehydrogenase)
to HMM TIGR01327 (serA: phosphoglycerate dehydrogenase (EC 1.1.1.95))

# 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/TIGR01327.hmm
# target sequence database:        /tmp/gapView.8857.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01327  [M=525]
Accession:   TIGR01327
Description: PGDH: phosphoglycerate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-192  626.3   0.1   2.6e-192  626.1   0.1    1.0  1  lcl|NCBI__GCF_900107645.1:WP_092350915.1  BLU87_RS16615 phosphoglycerate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900107645.1:WP_092350915.1  BLU87_RS16615 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  626.1   0.1  2.6e-192  2.6e-192       1     525 []       2     528 ..       2     528 .. 0.99

  Alignments for each domain:
  == domain 1  score: 626.1 bits;  conditional E-value: 2.6e-192
                                 TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 
                                               kvl++d++s++g+  l+++ ++++d k gls  el ++i  y+a+i+RS t v++ ll+ a++Lk+++R
  lcl|NCBI__GCF_900107645.1:WP_092350915.1   2 KVLITDEISDNGLLpLTEDPRIHIDKKLGLSIPELHKIIGGYEAIITRSGTLVDKALLDCADNLKIVAR 70 
                                               7***********999****************************************************** PP

                                 TIGR01327  69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137
                                               aGvG+DN+d++aa+ kGi+vvNaP gn  saaE+++a++l+l R++p a++s+k + W+r  f+G El+
  lcl|NCBI__GCF_900107645.1:WP_092350915.1  71 AGVGIDNVDVDAASSKGIIVVNAPYGNVNSAAEHTMAIMLSLFRNVPMANTSLKGGDWKRALFTGCELK 139
                                               ********************************************************************* PP

                                 TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206
                                               gkt+G+iGlG++G +va+r++a++++v++yDPyise++a+++gv+ l+ l+++++ +DvitvH+Pl++e
  lcl|NCBI__GCF_900107645.1:WP_092350915.1 140 GKTVGIIGLGKVGGRVARRCRAFEAEVITYDPYISEKRADDFGVK-LQPLEDIIRFSDVITVHTPLNDE 207
                                               *********************************************.788******************** PP

                                 TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt...dnklleldnv 272
                                               t+++i+ ++++ mK+gv+i+NcaRGGii+E+A++eale+gk ++aa+Dv+++EPp+    +kl++++++
  lcl|NCBI__GCF_900107645.1:WP_092350915.1 208 TRNIISSDSFKGMKDGVVIINCARGGIINEAAMLEALESGKCAGAAFDVWSQEPPKtdvLQKLIAHPKM 276
                                               *******************************************************9877799******* PP

                                 TIGR01327 273 vvtpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqll 341
                                                vtpHlgA+t Eaq+nvav+v++e+++++ g + e+avN+p  d +++e++kp+++l+  lG ++sql+
  lcl|NCBI__GCF_900107645.1:WP_092350915.1 277 LVTPHLGANTFEAQKNVAVDVSKEIVNYVDGRPLENAVNIPRFDPDQMEHMKPFMQLVSILGDFISQLA 345
                                               ********************************************************************* PP

                                 TIGR01327 342 keavkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedykn 410
                                                 +++kv+ t++G+la+++  +l+ + l+ ll++ +++evn+vnA  +a+e gi+ve  ++ e++++++
  lcl|NCBI__GCF_900107645.1:WP_092350915.1 346 PPNPNKVTFTYNGQLARFDCAPLSVSGLAALLNHCTDQEVNMVNASLIAREMGIEVESIRSTETDSFSS 414
                                               ********************************************************************* PP

                                 TIGR01327 411 llevkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNi 479
                                               l+++ +e+++g++++agt++e+ +p+iv+++++ +d++pe+ +l+i+++D++G+igk+g++lgea++Ni
  lcl|NCBI__GCF_900107645.1:WP_092350915.1 415 LITLSLESAQGRRTIAGTLFEG-TPKIVKMRDYAIDFRPEKDMLVINYQDRSGLIGKIGTVLGEADVNI 482
                                               *********************5.********************************************** PP

                                 TIGR01327 480 asmqlgrkekggealmllslDeevseevleeikevpeiksvklvel 525
                                                +m+lgr+ek gea+++ s+D++v+ee l+++ e  + k +k+v+l
  lcl|NCBI__GCF_900107645.1:WP_092350915.1 483 GNMSLGRQEKAGEAMVVFSVDSPVDEETLQKVSEAVSPKFIKAVHL 528
                                               **********************************999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (531 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: 00:00:00.02
# Mc/sec: 11.48
//
[ok]

This GapMind analysis is from Apr 10 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