Alignments for a candidate for ramA in Desulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for ramA in Desulfovibrio gracilis DSM 16080

Align ATP-dependent reduction of co(II)balamin (RamA-like) (characterized)
to candidate WP_078716261.1 B5D49_RS03480 DUF4445 domain-containing protein

Query= reanno::Miya:8500650
         (685 letters)



>NCBI__GCF_900167125.1:WP_078716261.1
          Length = 518

 Score =  380 bits (975), Expect = e-109
 Identities = 249/634 (39%), Positives = 312/634 (49%), Gaps = 126/634 (19%)

Query: 55  AAEVTLPDGRILHLPLSQSVSLSGQAAAGAAPASTLAQLVWMSGQVDPPALCSGLGRCGR 114
           A  + LPDG I                A  +   TLAQ +++ G  +   LCSGLG+CG 
Sbjct: 3   AISIRLPDGTI--------------RTARPSQGQTLAQAIFLLGLWNDTPLCSGLGKCGL 48

Query: 115 CAARFTRGTPAPHPAEEAHFSPAELADGWRLLCRHALPAPASRSPSSPQGTDPNGNAASP 174
           C  RF    P P   E+      ++ +GWRL C H  PA  +R    P            
Sbjct: 49  CRVRFLADAPPPRREEKQRLGKKDVDNGWRLACLH--PAAPARIELPPS----------- 95

Query: 175 PDARCTMAFTLPAGSAPRRFRAADAPLPDAIQASATGTSPATYTSPATGTSPATGTSPAT 234
                      P G+APR                                       P  
Sbjct: 96  -----------PRGAAPRM-----------------------------------QGQPRP 109

Query: 235 GAPLLLAIDLGTTTLHWSALTPDGRRVAHGAELNPQMGAGSEVMSRLAVASSPQGLAALR 294
             P+ LA+D GTT+LHWSAL  +G   A G+ELN Q+G G E+M+RLA   +P G   LR
Sbjct: 110 NVPIRLAVDFGTTSLHWSALQ-NGEETASGSELNAQIGLGGEIMARLAFTQTPDGGRELR 168

Query: 295 RLTLAAVARIAAGLPGPVRGLCVAGNSAMTAILLGHDVSGLATAPYRLDYAGGTAEILPE 354
            L L  +  +AA L  P+  LCVA N AM A+LLG D SGL  APYR   +GG  E L  
Sbjct: 169 ELALGQLKHLAALLNTPLEELCVAANPAMLALLLGRDPSGLMAAPYRSPLSGGMWEELDP 228

Query: 355 LADVTYRAGLPDLPDSPGRAAVPEVWIPPQPAPFVGGDVGAGMAALLYGGLVSGGGAGVA 414
                               A+P  +IPP  APFVG D+ AG+AAL+             
Sbjct: 229 --------------------ALPPAYIPPVYAPFVGADLSAGLAALVL------------ 256

Query: 415 ANTLQAAATAPAPAASPRFPFLLADLGTNGEFVLATGPDSALVTSVALGPALEGIGLSCG 474
                      AP A P +PFLLADLGTNGEF+LA  P  AL  SV +GPALEG+GL  G
Sbjct: 257 -----------APNAQPDYPFLLADLGTNGEFILALSPREALCASVPMGPALEGVGLRHG 305

Query: 475 GVAQPGAIAAFTLGPAGLAPTVLPED-DGAPAAPTHLCGTGYLSLLRVLLRAGLLDEDGR 533
             A PGA+  FTL P G+ PT       G P     + GTG+LSL  +L R GLL  +G 
Sbjct: 306 RTAGPGAVTGFTLTPRGVTPTYFESRRQGIPG----ITGTGHLSLAALLRRNGLLTTEGL 361

Query: 534 FVMEPHS---PLARRLAASLVEVRGERRLPLPGGLHLSAGDVEEVLKVKAAFSLAYERLL 590
           F  +      PL   L  SL  ++GE    LP GLHL   D+EE+LKVKAAF+LA+ RLL
Sbjct: 362 FTPQADPAAPPLQHILRKSLDTLQGEPVFQLPDGLHLPGSDIEEMLKVKAAFNLAFSRLL 421

Query: 591 AEAGMSGTALDAVYLAGALGEHARPDDLETLGFLPAGVAGRTRAVGNASLRGAELLLLQP 650
            EAG+  + L A++LAGA+GEH  P DLETLGF+P G A + R+ GN SLRGA LLL  P
Sbjct: 422 KEAGLQSSRLKAIHLAGAMGEHVAPGDLETLGFVPTGAAEKIRSQGNTSLRGARLLLQSP 481

Query: 651 ELRARINAWRTGCRVVDLTTASDFSAAFLRHMRF 684
           E R+ + A      +VDL    +    F++ M F
Sbjct: 482 ETRSALEA-LPHPTLVDLAADPELGQQFMQRMVF 514


Lambda     K      H
   0.316    0.133    0.403 

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: 1224
Number of extensions: 81
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 685
Length of database: 518
Length adjustment: 37
Effective length of query: 648
Effective length of database: 481
Effective search space:   311688
Effective search space used:   311688
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: 53 (25.0 bits)

Align candidate WP_078716261.1 B5D49_RS03480 (DUF4445 domain-containing 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.2733.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    9.1e-45  138.8   0.0    1.3e-44  138.3   0.0    1.1  1  lcl|NCBI__GCF_900167125.1:WP_078716261.1  B5D49_RS03480 DUF4445 domain-con


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078716261.1  B5D49_RS03480 DUF4445 domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.3   0.0   1.3e-44   1.3e-44       4     251 ..     267     516 ..     265     518 .] 0.90

  Alignments for each domain:
  == domain 1  score: 138.3 bits;  conditional E-value: 1.3e-44
                                RACo_C_ter   4 lliDiGTNaEivlg.nkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignekp 71 
                                               ll D+GTN+E +l  +  + l+as + GPAlEG ++++G +A pgA+  ++++p+ +++++    ++ +
  lcl|NCBI__GCF_900167125.1:WP_078716261.1 267 LLADLGTNGEFILAlSPREALCASVPMGPALEGVGLRHGRTAGPGAVTGFTLTPRGVTPTYFESRRQGI 335
                                               899*******9997245678999*****************************************99*** PP

                                RACo_C_ter  72 kGicGsGiidliaelleagiidkkgklnkel..kserireeeeteeyvlvlaeesetekdivitekDid 138
                                                Gi+G+G ++l a l ++g+++++g ++ ++  + + +++  ++   +l+ +   +  + + +  +Di+
  lcl|NCBI__GCF_900167125.1:WP_078716261.1 336 PGITGTGHLSLAALLRRNGLLTTEGLFTPQAdpAAPPLQHILRKSLDTLQGEPVFQLPDGLHLPGSDIE 404
                                               ***************************998744344444444555555555555566779********* PP

                                RACo_C_ter 139 elirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslag 207
                                               e+++ kaA + +++ Ll+e+gl+ ++++ + laGa+G+++ + +  t+G +P+ ++ek+++ GNtsl+g
  lcl|NCBI__GCF_900167125.1:WP_078716261.1 405 EMLKVKAAFNLAFSRLLKEAGLQSSRLKAIHLAGAMGEHVAPGDLETLGFVPTGAAEKIRSQGNTSLRG 473
                                               ********************************************************************* PP

                                RACo_C_ter 208 AraallsreareeleeiarkityielavekkFmeefvaalflph 251
                                               Ar +l s+e+r+ le++ +  t ++la++++  ++f++ + + h
  lcl|NCBI__GCF_900167125.1:WP_078716261.1 474 ARLLLQSPETRSALEALPH-PTLVDLAADPELGQQFMQRMVFDH 516
                                               ************9999875.589*****************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (518 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: 00:00:00.00
# Mc/sec: 18.71
//
[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