Alignments for a candidate for serA in Desulfoscipio geothermicus DSM 3669

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Desulfoscipio geothermicus DSM 3669

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_092487414.1 BM299_RS17355 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_900115975.1:WP_092487414.1
          Length = 529

 Score =  476 bits (1226), Expect = e-139
 Identities = 242/525 (46%), Positives = 352/525 (67%), Gaps = 4/525 (0%)

Query: 3   KILITDPLHESAVEILKQAGEVEVATG--LTVEELKLKIKDVDALVIRSGTTATREIIEA 60
           K+L  D + E  +E L++  ++EV  G  +T +EL   I D DA+++RS T  T  ++E 
Sbjct: 5   KVLAMDNVSEKGLEPLRKEPDIEVVIGKKMTEDELVEIIGDYDAMIVRSATKVTPRVLEN 64

Query: 61  SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120
           +  LKV+ RAGVGVDN+DL+AAT+ G++VVNAPD ++I+  E    MMLA ARNIPQA A
Sbjct: 65  APKLKVVGRAGVGVDNIDLNAATQHGVLVVNAPDGNTIAATEHTIAMMLALARNIPQAVA 124

Query: 121 SIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180
            +K+G WD+K+F G+E+ GK LG++GLGRIG  VA+RAQA  M IVAYDPYI  + A  L
Sbjct: 125 KMKNGVWDKKAFLGVELRGKVLGVIGLGRIGSAVARRAQALEMDIVAYDPYITSEKAESL 184

Query: 181 GIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALY 240
           GIKL+T+DEL  V+DFIT+H+P T +T HM+ ++  A MK  + ++NCARGG++DE ALY
Sbjct: 185 GIKLVTMDELLPVADFITMHMPKTKETYHMLDEQAFAKMKDGVRVINCARGGIVDEEALY 244

Query: 241 DALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI 300
             + SGK+  AALDVFE+EP  ESPLL L+N I TPH GAST EAQL+    VAE+ V+ 
Sbjct: 245 KYMQSGKVAGAALDVFEKEPNTESPLLALDNFIATPHLGASTAEAQLNVAIDVAEEIVEA 304

Query: 301 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKEK 360
           L+G+   N VN+P V  E M K+KPY+ LAEK+G    Q ++     LE+TY G LA E+
Sbjct: 305 LQGKVVRNTVNIPSVKPEVMVKIKPYLKLAEKLGKFQAQLVEGRATKLEVTYNGDLAGEE 364

Query: 361 TEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSES-DYGNSIKISAKGEN 419
            + +  + +KG L PIL   VN +NAP++AK+R I + +     +  Y + I +    + 
Sbjct: 365 VKPITTALIKGFLDPILQETVNFINAPLLAKNRGINVIQTVNGRAGGYASLITVKVVSDK 424

Query: 420 DEISIIGSI-EHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIA 478
            E ++ G++ + N+     ++GYR+D  PEG +  + HID+P ++G VG++ G++ INIA
Sbjct: 425 GEHTLSGTLFQDNDPRIVMVDGYRVDAIPEGYMLYVPHIDKPMIIGPVGMMFGKYNINIA 484

Query: 479 GMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSINI 523
            MQVGR+E GG ++M L +D  + ++ + EI  ++ V   K +++
Sbjct: 485 SMQVGRKEVGGKAVMMLSVDAPVPEDTMKEIAGIDGVLDVKFVSL 529


Lambda     K      H
   0.316    0.134    0.364 

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: 785
Number of extensions: 34
Number of successful extensions: 4
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: 523
Length of database: 529
Length adjustment: 35
Effective length of query: 488
Effective length of database: 494
Effective search space:   241072
Effective search space used:   241072
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_092487414.1 BM299_RS17355 (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.26336.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-220  717.9  10.7   4.4e-220  717.8  10.7    1.0  1  NCBI__GCF_900115975.1:WP_092487414.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900115975.1:WP_092487414.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  717.8  10.7  4.4e-220  4.4e-220       1     525 []       5     529 .]       5     529 .] 0.99

  Alignments for each domain:
  == domain 1  score: 717.8 bits;  conditional E-value: 4.4e-220
                             TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvG 72 
                                           kvl  d++se+g+e l ke ++ev + ++++++el+e+i dyda+ivRSatkvt  +le+a+kLkv+gRaGvG
  NCBI__GCF_900115975.1:WP_092487414.1   5 KVLAMDNVSEKGLEpLRKEPDIEVVIGKKMTEDELVEIIGDYDAMIVRSATKVTPRVLENAPKLKVVGRAGVG 77 
                                           7999**********9999******************************************************* PP

                             TIGR01327  73 vDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviG 145
                                           vDNid++aat++G+lvvNaP+gnti+a+E+++a++lalaR+ipqa +++k++ W++k+flG+El+gk lGviG
  NCBI__GCF_900115975.1:WP_092487414.1  78 VDNIDLNAATQHGVLVVNAPDGNTIAATEHTIAMMLALARNIPQAVAKMKNGVWDKKAFLGVELRGKVLGVIG 150
                                           ************************************************************************* PP

                             TIGR01327 146 lGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelak 218
                                           lGriGs va+ra+al+m+++ayDPyi++ekae+lg++ l ++dell  aD+it+H+P+tket ++++++++ak
  NCBI__GCF_900115975.1:WP_092487414.1 151 LGRIGSAVARRAQALEMDIVAYDPYITSEKAESLGIK-LVTMDELLPVADFITMHMPKTKETYHMLDEQAFAK 222
                                           *************************************.667******************************** PP

                             TIGR01327 219 mKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvav 291
                                           mK+gv+++NcaRGGi+dE+AL++++++gkv++aalDvfekEP t+++ll+ldn ++tpHlgAst+Eaq nva+
  NCBI__GCF_900115975.1:WP_092487414.1 223 MKDGVRVINCARGGIVDEEALYKYMQSGKVAGAALDVFEKEPNTESPLLALDNFIATPHLGASTAEAQLNVAI 295
                                           ************************************************************************* PP

                             TIGR01327 292 evaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesell 364
                                           +vaee++eal+g+vv+++vN+p+++ e++ k+kpyl+laeklGk+  ql++++ +k+evt++G+la ee++++
  NCBI__GCF_900115975.1:WP_092487414.1 296 DVAEEIVEALQGKVVRNTVNIPSVKPEVMVKIKPYLKLAEKLGKFQAQLVEGRATKLEVTYNGDLAGEEVKPI 368
                                           ************************************************************************* PP

                             TIGR01327 365 tsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepri 437
                                           t+al+kg+l+++l+e+vn++nA+ +ak+rgi+v ++ +  +  y +l++vkv +dkge++++gt+++++ pri
  NCBI__GCF_900115975.1:WP_092487414.1 369 TTALIKGFLDPILQETVNFINAPLLAKNRGINVIQTVNGRAGGYASLITVKVVSDKGEHTLSGTLFQDNDPRI 441
                                           ************************************************************************* PP

                             TIGR01327 438 veidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevlee 510
                                           v +dg++vd  peg++l++ + Dkp +ig vg+++g+++iNiasmq+grke gg+a+m+ls+D +v+e+ ++e
  NCBI__GCF_900115975.1:WP_092487414.1 442 VMVDGYRVDAIPEGYMLYVPHIDKPMIIGPVGMMFGKYNINIASMQVGRKEVGGKAVMMLSVDAPVPEDTMKE 514
                                           ************************************************************************* PP

                             TIGR01327 511 ikevpeiksvklvel 525
                                           i+ ++ + +vk v+l
  NCBI__GCF_900115975.1:WP_092487414.1 515 IAGIDGVLDVKFVSL 529
                                           ***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (529 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: 21.66
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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