Alignments for a candidate for asnB in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Azospirillum brasilense Sp245

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate AZOBR_RS22535 AZOBR_RS22535 asparagine synthase

Query= CharProtDB::CH_007942
         (614 letters)



>FitnessBrowser__azobra:AZOBR_RS22535
          Length = 591

 Score =  246 bits (627), Expect = 3e-69
 Identities = 189/587 (32%), Positives = 287/587 (48%), Gaps = 43/587 (7%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDI-EGG 59
           MCGI+G + F  +       +  MT+ L+ RGPD   V+    + FGH+RL+++D+ E  
Sbjct: 1   MCGISGEIRFDSRPASAS-AVGSMTEALALRGPDGQGVFAHGRMAFGHRRLSIIDLSEAA 59

Query: 60  RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119
           +QPM     G    I++NG +YN  +LR EL A+G++F    DTEVLL +Y  W    V+
Sbjct: 60  QQPMTDPELG--LGIVFNGCIYNYPELRAELEAKGYRFFSHGDTEVLLKAYHAWGRRFVE 117

Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179
            L G+FAFA+W+     +   RDRLG+KP + ++      F S + A+LA  DI   +D 
Sbjct: 118 RLYGMFAFAIWERDSGRVTLGRDRLGIKPLYLSETAGRLRFASTLPALLAGGDIDTTIDP 177

Query: 180 TGLSEIFGL-GPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWR-YWN-VESEKHTD--- 233
            GL +          PGT I KG++++ PA  LT   DG  I   YW  V      D   
Sbjct: 178 VGLYQYMSFHAVVPAPGT-ILKGVRKLPPATLLTLEPDGRRIEETYWEPVFGPPPGDERM 236

Query: 234 SFDDTVANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYS 293
           S  D    V S  + AV R+LV+DVPV   LSGGLDSS I A+ A    + G+  L T+S
Sbjct: 237 SEGDWQDAVLSTLRKAVERRLVADVPVGVLLSGGLDSSVIVALLA----EAGQTGLQTFS 292

Query: 294 IDYEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPG 353
           I +E   +       +  D+  + + + + F T HHK  I     +  L++ V     P 
Sbjct: 293 IGFETVGQ-------EKGDEFQYSDLIAQRFQTDHHKLFIDSNRALPALQDCVRAMSEPM 345

Query: 354 MADVDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWF----HTADVESGFP---WMRST 406
           ++          +E+ K   V  SG+ ADEIF GY W+      AD  S +    + R+ 
Sbjct: 346 VSHDAIGFFLLSQEVAKHVKVVQSGQGADEIFAGYHWYPPMMEAADPLSTYAKVFFDRNR 405

Query: 407 EERIKLLSDSWQKKLN-LKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLNMLWFMTN 465
            E  + L+  +    +    +V A +    A+ P       VDKA R       +  + +
Sbjct: 406 AEMAEALNPQYLADEDAASAFVAAHFARPGADRP-------VDKALR---LDTTVMLVDD 455

Query: 466 LLDRKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGILPDDIL 525
            + R D M+M   LE RVPF DH LVE    +P E+K+ D   K +L++A   ++P +++
Sbjct: 456 PVKRVDNMTMAWGLEGRVPFLDHDLVELAARVPPELKVRDG-GKYVLKEAARKVVPSEVI 514

Query: 526 YRKKSPYPKTHHPEYTKG-VSEWLKTIRSQKDSVLHTLLDRKQLDQL 571
            R K  +P     +Y +G   E ++ + +Q  +    L     LD+L
Sbjct: 515 DRPKGYFP-VPALKYLRGPYLELVRDVLNQPAARKRALFQPAYLDRL 560


Lambda     K      H
   0.320    0.137    0.425 

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: 848
Number of extensions: 38
Number of successful extensions: 6
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: 614
Length of database: 591
Length adjustment: 37
Effective length of query: 577
Effective length of database: 554
Effective search space:   319658
Effective search space used:   319658
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 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate AZOBR_RS22535 AZOBR_RS22535 (asparagine synthase)
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.15892.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.5e-139  449.9   0.0   8.5e-139  449.7   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS22535  AZOBR_RS22535 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS22535  AZOBR_RS22535 asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.7   0.0  8.5e-139  8.5e-139       1     516 [.       2     520 ..       2     521 .. 0.91

  Alignments for each domain:
  == domain 1  score: 449.7 bits;  conditional E-value: 8.5e-139
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cgi g +  +   ++  +a+ +m+e+la RGPD++gv+ +    + ++ghrRL+iidlse+ +QP+ + 
  lcl|FitnessBrowser__azobra:AZOBR_RS22535   2 CGISGEIRFDSRPAS-ASAVGSMTEALALRGPDGQGVFAH---GRMAFGHRRLSIIDLSEAaQQPMTDP 66 
                                               ********9887776.49**********************...8****************99******* PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgel 136
                                               +    ivfnG IYN+ eLr+ele+kGy+F ++ DtEV+L+ay++wg+++verL GmFAfa+w++ +g++
  lcl|FitnessBrowser__azobra:AZOBR_RS22535  67 ElGLGIVFNGCIYNYPELRAELEAKGYRFFSHGDTEVLLKAYHAWGRRFVERLYGMFAFAIWERDSGRV 135
                                               **99***************************************************************** PP

                                 TIGR01536 137 flaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkele 204
                                                l RDrlGikPLY ++++g+l faS + alla  +i++ +d  +l ++++++ +vp + t+ k+v++l+
  lcl|FitnessBrowser__azobra:AZOBR_RS22535 136 TLGRDRLGIKPLYLSETAGRLRFASTLPALLAGGDIDTTIDPVGLYQYMSFHaVVPAPGTILKGVRKLP 204
                                               ****************************************************999************** PP

                                 TIGR01536 205 pakal....dgeekleeywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDS 265
                                               pa  l    dg +  e+ywe          ++se +  + + ++l++av++rlvadvpvgvllSGGlDS
  lcl|FitnessBrowser__azobra:AZOBR_RS22535 205 PATLLtlepDGRRIEETYWEPVFGPppgdERMSEGDWQDAVLSTLRKAVERRLVADVPVGVLLSGGLDS 273
                                               ****9997555555555***999888888999999********************************** PP

                                 TIGR01536 266 slvaaiakkeaksevktFsigfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilale 332
                                               s+++a++++  ++ ++tFsigfe  ++++ de ++   +a+ + t+h+++ i+++ +l +l++ ++a+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS22535 274 SVIVALLAEAGQTGLQTFSIGFEtvGQEKGDEFQYSDLIAQRFQTDHHKLFIDSNRALPALQDCVRAMS 342
                                               ***********************9889999999************************************ PP

                                 TIGR01536 333 eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekkl..llq 399
                                               ep+  +++i+ +lls+++ ++ vkVv sG+GaDE+f+GY+++  +  +++   ++     +k +  + +
  lcl|FitnessBrowser__azobra:AZOBR_RS22535 343 EPMVSHDAIGFFLLSQEVAKH-VKVVQSGQGADEIFAGYHWYPPMMEAADPL-ST----YAKVFfdRNR 405
                                               *********************.********************9874444432.22....2222311333 PP

                                 TIGR01536 400 aklakeselkellkakleeelkekeelkkelkeeseleellrldlelllsdl.lrakDrvsmahslEvR 467
                                               a++a++ +      a+ +++++ + +++++  +++ ++++lrld++ +l d+ +++ D ++ma++lE R
  lcl|FitnessBrowser__azobra:AZOBR_RS22535 406 AEMAEALNP--QYLADEDAASAFVAAHFARPGADRPVDKALRLDTTVMLVDDpVKRVDNMTMAWGLEGR 472
                                               333333333..33445667777788888888888***********998877626666************ PP

                                 TIGR01536 468 vPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKea 516
                                               vPflD++lvela+++ppelk+rdg  K++L+eaa++++P+e+ +R+K  
  lcl|FitnessBrowser__azobra:AZOBR_RS22535 473 VPFLDHDLVELAARVPPELKVRDG-GKYVLKEAARKVVPSEVIDRPKGY 520
                                               **********************98.7********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (591 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: 12.16
//
[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