Alignments for a candidate for ramA in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Phaeobacter inhibens BS107

Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate GFF1501 PGA1_c15200 Uncharacterized metal-binding protein

Query= reanno::Phaeo:GFF1501
         (698 letters)



>FitnessBrowser__Phaeo:GFF1501
          Length = 698

 Score = 1388 bits (3592), Expect = 0.0
 Identities = 698/698 (100%), Positives = 698/698 (100%)

Query: 1   MANDPAPEISTETATDPASHPLVVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGI 60
           MANDPAPEISTETATDPASHPLVVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGI
Sbjct: 1   MANDPAPEISTETATDPASHPLVVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGI 60

Query: 61  CSKCQITPSYGEFSKHGVTVADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVID 120
           CSKCQITPSYGEFSKHGVTVADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVID
Sbjct: 61  CSKCQITPSYGEFSKHGVTVADDALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVID 120

Query: 121 VPPESQVHRQVVRKRAEARDITMNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLK 180
           VPPESQVHRQVVRKRAEARDITMNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLK
Sbjct: 121 VPPESQVHRQVVRKRAEARDITMNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDLK 180

Query: 181 GVKTDLHILSVLQPALRKGGWKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGST 240
           GVKTDLHILSVLQPALRKGGWKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGST
Sbjct: 181 GVKTDLHILSVLQPALRKGGWKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGST 240

Query: 241 TIAAHLCDLKTGDVVASSGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALF 300
           TIAAHLCDLKTGDVVASSGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALF
Sbjct: 241 TIAAHLCDLKTGDVVASSGIMNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALF 300

Query: 301 TQIAAEAEIDKALIVDAVFVCNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLN 360
           TQIAAEAEIDKALIVDAVFVCNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLN
Sbjct: 301 TQIAAEAEIDKALIVDAVFVCNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLN 360

Query: 361 IHPAARVYLLPCIAGHVGADAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACS 420
           IHPAARVYLLPCIAGHVGADAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACS
Sbjct: 361 IHPAARVYLLPCIAGHVGADAAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACS 420

Query: 421 SPTGPAFEGAQISSGQRAAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGI 480
           SPTGPAFEGAQISSGQRAAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGI
Sbjct: 421 SPTGPAFEGAQISSGQRAAPGAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGI 480

Query: 481 TGICGSGIIEAIAEMRMAGLLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTI 540
           TGICGSGIIEAIAEMRMAGLLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTI
Sbjct: 481 TGICGSGIIEAIAEMRMAGLLDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTI 540

Query: 541 TVTNPDIRAIQMAKAALYSGARLLMDKFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDC 600
           TVTNPDIRAIQMAKAALYSGARLLMDKFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDC
Sbjct: 541 TVTNPDIRAIQMAKAALYSGARLLMDKFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDC 600

Query: 601 PLDKVTSAGNAAGTGARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPNS 660
           PLDKVTSAGNAAGTGARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPNS
Sbjct: 601 PLDKVTSAGNAAGTGARIALLNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPNS 660

Query: 661 AEPFPILSSIVTLPEANFNTGGGDGNEVGGRRRRRRRG 698
           AEPFPILSSIVTLPEANFNTGGGDGNEVGGRRRRRRRG
Sbjct: 661 AEPFPILSSIVTLPEANFNTGGGDGNEVGGRRRRRRRG 698


Lambda     K      H
   0.318    0.135    0.396 

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: 1554
Number of extensions: 37
Number of successful extensions: 1
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: 698
Length of database: 698
Length adjustment: 39
Effective length of query: 659
Effective length of database: 659
Effective search space:   434281
Effective search space used:   434281
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate GFF1501 PGA1_c15200 (Uncharacterized metal-binding protein)
to HMM PF14574 (RACo_C_ter)

# 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/PF14574.10.hmm
# target sequence database:        /tmp/gapView.24684.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       RACo_C_ter  [M=261]
Accession:   PF14574.10
Description: C-terminal domain of RACo the ASKHA domain
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-91  292.0   1.1    2.3e-91  291.5   1.1    1.2  1  lcl|FitnessBrowser__Phaeo:GFF1501  PGA1_c15200 Uncharacterized meta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1501  PGA1_c15200 Uncharacterized metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.5   1.1   2.3e-91   2.3e-91       2     258 ..     396     665 ..     395     668 .. 0.94

  Alignments for each domain:
  == domain 1  score: 291.5 bits;  conditional E-value: 2.3e-91
                         RACo_C_ter   2 islliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek....... 70 
                                        ++l++D+GTNaEi lgnkd++la+s+++GPA+EG++i++G+rAapgAiervei+pet e++++vig++        
  lcl|FitnessBrowser__Phaeo:GFF1501 396 LVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISSGQRAAPGAIERVEINPETKEPRFRVIGSDIwsdedgf 471
                                        689**************************************************************998889999** PP

                         RACo_C_ter  71 ........pkGicGsGiidliaelleagiidkkgklnkel..kserireeeeteeyvlvlaeesetekdivitekD 136
                                                ++GicGsGii++iae+  ag++d +g + +     ++r+ ++ +t++y+l +  + e +  i++t+ D
  lcl|FitnessBrowser__Phaeo:GFF1501 472 aaavattgITGICGSGIIEAIAEMRMAGLLDASGLIGSAEqtGTTRCIQDGRTNAYLLWDG-SVEGGPTITVTNPD 546
                                        ***********************************98776225566667778888887665.566678******** PP

                         RACo_C_ter 137 idelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagAraal 212
                                        i+++++akaA+y+g+++L++++g  ++ +d+v+laGafG++i +++A+++G++Pd++l+kv+++GN++++gAr+al
  lcl|FitnessBrowser__Phaeo:GFF1501 547 IRAIQMAKAALYSGARLLMDKFG--IDTVDRVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTGARIAL 620
                                        ***********************..99************************************************* PP

                         RACo_C_ter 213 lsreareeleeiarkityielavekkFmeefvaalflphtdlelfp 258
                                        l++ear+e+e+ +++i++ie+ave++F+e+fv+a ++p+ ++e+fp
  lcl|FitnessBrowser__Phaeo:GFF1501 621 LNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPN-SAEPFP 665
                                        **************************************9.555887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (698 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 13.92
//
[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