Alignments for a candidate for asnB in Desulfuromonas acetexigens DSM 1397

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Desulfuromonas acetexigens DSM 1397

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_092056330.1 BQ4888_RS08335 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_900111775.1:WP_092056330.1
          Length = 627

 Score =  390 bits (1002), Expect = e-113
 Identities = 220/631 (34%), Positives = 356/631 (56%), Gaps = 33/631 (5%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G++N   L     + E + +MN  ++HRGPD  G F D  VG G RRL+IID+  
Sbjct: 1   MCGICGIYN---LTGAPVERERLGRMNDTLIHRGPDGAGLFVDGAVGLGHRRLAIIDLHT 57

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QP++ +D    ++FNGEIYN+ EL++ELEA G+ F T SDTEV+L  YR + E    +
Sbjct: 58  GEQPMATDDGRLQVVFNGEIYNFRELKQELEAHGHRFRTHSDTEVILHGYRQWGEAVVDR 117

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQN-DIEIDKE 179
           LRGMFA  +W+  +  L   RD  G KPLYY     ++ F SE K+L+  +     +D  
Sbjct: 118 LRGMFAIALWDAPNRTLLLVRDRLGKKPLYYHFDGSRMVFGSEMKALLTDETLPRTLDPA 177

Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYF--KANFKPVQTEEDKL 237
           A+  Y SF +VP P ++   ++K+ P +   +   G ++ + Y+    N +P +  E + 
Sbjct: 178 AVDAYCSFGYVPSPMSIFKEIRKLPP-AHLAVVSSGGLSLRRYWDLDMNREPEEVPEARA 236

Query: 238 VKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIV-SVAKEFHPSLKTFSVGFEQQGFS 296
           + E+R+   ++V + M SDVP+G+FLSGG+DSS +V S++ +    ++T ++GF ++ F+
Sbjct: 237 LAELREVFDEAVRLRMISDVPLGAFLSGGVDSSAVVASMSLQGGAPVRTAAIGFAEKRFN 296

Query: 297 EVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKKHV 356
           E++ A+  A   G E+   V+ PE  +  + ++VWHFD+P AD +A+P ++V++ A++ V
Sbjct: 297 ELEYAEVVARRYGAEHHEFVVRPEA-LEIIDRLVWHFDEPFADSSAVPTWYVSQMARQRV 355

Query: 357 TVALSGEGADELFGGYNIYREPLSLKPFE-----RIPSGLKKMLLHVAA-------VMPE 404
           TVALSG+G DE F GY       ++  FE     +IP+ L+  LL   A        +P 
Sbjct: 356 TVALSGDGGDETFAGYT---RRYAMTRFEDGLRRKIPASLRTGLLGPLARIYPRADFLPR 412

Query: 405 GMRGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYR-------DVTKTYFT 457
            +R K  L     PL+  Y  +   + +   K LL  Y P  + +        V   +F 
Sbjct: 413 PLRLKGFLTNLSLPLEQAYFRDMSFYCKPEAKALL--YTPEFTAQVGASRAEAVLGAHFA 470

Query: 458 ESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELK 517
            + +   +++ QYVDIH+++  DIL+K D+M+MA+SLE+R P LD  V + A+++P   K
Sbjct: 471 RNRNPDPVSRAQYVDIHSYLPEDILVKVDRMSMAHSLEVRAPILDHKVLEFAARLPSTQK 530

Query: 518 TKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIH 577
            +   +KY+ +K  E  +P  +L RKK GF VP+  WL+ E+ E   + +     D   +
Sbjct: 531 LRGEQSKYIFKKMNEDRLPADILYRKKQGFSVPLDEWLRGELRELAHDSLFNGGLDGLFN 590

Query: 578 KDYVLQLLEDHCADKADNSRKIWTVLIFMIW 608
             +V +L + H + +  N   +W +L+F  W
Sbjct: 591 GTHVRRLWDAHQSGREHNGTPLWGLLMFSRW 621


Lambda     K      H
   0.319    0.136    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: 987
Number of extensions: 43
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: 632
Length of database: 627
Length adjustment: 38
Effective length of query: 594
Effective length of database: 589
Effective search space:   349866
Effective search space used:   349866
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: 54 (25.4 bits)

Align candidate WP_092056330.1 BQ4888_RS08335 (asparagine synthase (glutamine-hydrolyzing))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# 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/TIGR01536.hmm
# target sequence database:        /tmp/gapView.1923561.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-154  502.1   0.0   1.4e-154  501.8   0.0    1.1  1  NCBI__GCF_900111775.1:WP_092056330.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900111775.1:WP_092056330.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.8   0.0  1.4e-154  1.4e-154       1     517 []       2     560 ..       2     560 .. 0.88

  Alignments for each domain:
  == domain 1  score: 501.8 bits;  conditional E-value: 1.4e-154
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cgi gi +l+ + +e +e + +m++tl hRGPD+ g++ d    +++lghrRLaiidl++g+QP++ ++ + +
  NCBI__GCF_900111775.1:WP_092056330.1   2 CGICGIYNLTGAPVE-RERLGRMNDTLIHRGPDGAGLFVD---GAVGLGHRRLAIIDLHTGEQPMATDDgRLQ 70 
                                           *********987665.69**********************...8***************************** PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           +vfnGEIYN++eL++ele++G++F+t+sDtEViL+ y++wge++v+rL+GmFA+alwd+ +++l+l+RDrlG+
  NCBI__GCF_900111775.1:WP_092056330.1  71 VVFNGEIYNFRELKQELEAHGHRFRTHSDTEVILHGYRQWGEAVVDRLRGMFAIALWDAPNRTLLLVRDRLGK 143
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekl 215
                                           kPLYy  ++++++f+SE+Kall+ ++ ++ ld +a+  + ++ +vp++ ++fke+++l+pa+ +   +g  +l
  NCBI__GCF_900111775.1:WP_092056330.1 144 KPLYYHFDGSRMVFGSEMKALLTDETLPRTLDPAAVDAYCSFGYVPSPMSIFKEIRKLPPAHLAvvsSGGLSL 216
                                           **************************************************************99998899999 PP

                             TIGR01536 216 eeywevekee..vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsig 286
                                           ++yw++++++   +  e ++ +elre + +av+ r+++dvp+g++lSGG+DSs+v+a ++ +  ++v+t +ig
  NCBI__GCF_900111775.1:WP_092056330.1 217 RRYWDLDMNRepEEVPEARALAELREVFDEAVRLRMISDVPLGAFLSGGVDSSAVVASMSLQGGAPVRTAAIG 289
                                           99***99998445556678899****************************************99********* PP

                             TIGR01536 287 fedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvL 359
                                           f+ +k ++e ++a+ va+  g eh+e+++ +e +l+ +++++++++ep+a+++++p++ +s++ar++ v+V+L
  NCBI__GCF_900111775.1:WP_092056330.1 290 FA-EKRFNELEYAEVVARRYGAEHHEFVVRPE-ALEIIDRLVWHFDEPFADSSAVPTWYVSQMARQR-VTVAL 359
                                           **.*************************9875.689*******************************.***** PP

                             TIGR01536 360 sGeGaDElfgGYe.yfreakaeeale..................................lpeaselaekkl. 396
                                           sG+G+DE f+GY  ++    +e  l+                                  l          + 
  NCBI__GCF_900111775.1:WP_092056330.1 360 SGDGGDETFAGYTrRYAMTRFEDGLRrkipaslrtgllgplariypradflprplrlkgfL----------Tn 422
                                           ************7257777777777789888888888888887777777655555544432..........03 PP

                             TIGR01536 397 .........llqaklakeselkellka.kleeel..kekeelkkelkee.......seleellrldlelllsd 450
                                                    + + ++  + e k ll + ++++++  ++ e++ ++   +         ++++++ d++ +l++
  NCBI__GCF_900111775.1:WP_092056330.1 423 lslpleqayFRDMSFYCKPEAKALLYTpEFTAQVgaSRAEAVLGA---HfarnrnpDPVSRAQYVDIHSYLPE 492
                                           333333333444555444444444432022222200222222222...1334577799*************** PP

                             TIGR01536 451 llrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           ++++k Dr+smahslEvR+P+lD++++e+a+++p   klr ++ K++++++ e+ lP +il+RkK++f
  NCBI__GCF_900111775.1:WP_092056330.1 493 DILVKvDRMSMAHSLEVRAPILDHKVLEFAARLPSTQKLRGEQSKYIFKKMNEDRLPADILYRKKQGF 560
                                           ******************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (627 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: 19.69
//
[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