Alignments for a candidate for hisC in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Magnetospirillum magneticum AMB-1

Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate WP_011386328.1 AMB_RS20110 histidinol-phosphate aminotransferase

Query= reanno::azobra:AZOBR_RS20485
         (364 letters)



>NCBI__GCF_000009985.1:WP_011386328.1
          Length = 363

 Score =  442 bits (1138), Expect = e-129
 Identities = 228/362 (62%), Positives = 274/362 (75%), Gaps = 7/362 (1%)

Query: 8   PAPRPGILDIAPYVGGEHAGH-----IRLASNEGALGPSPRAVEAYRAAAGELHRYPDGG 62
           PAPRPGI+DI PYVGGE A       ++L+SNEGALGPSP+A+EA RA A E+HRYPDGG
Sbjct: 4   PAPRPGIMDIRPYVGGESAIEGVDRILKLSSNEGALGPSPKAMEALRAMAPEMHRYPDGG 63

Query: 63  SAKLRKAIAERFGLDADRVVCGAGSDELIALLIRAYAGPGDEVLYSQHGFLMYPIGAKSV 122
           +  LRKAI  RFGLDA R+VCGAGSDEL+ +L RAYAGPGDEVLYS HGFLMY I AK+ 
Sbjct: 64  AEDLRKAIGARFGLDASRIVCGAGSDELLGILCRAYAGPGDEVLYSAHGFLMYAIAAKAC 123

Query: 123 GATPVQAPETNLTTDVDSLLAHVTPRTRLVFVANPNNPTGTYITADEMARLHAGLPENAI 182
           GATPV APE +LT +VD+LLA VTPRT+++F+ANPNNPTGTY+ A E+ARL AGL  + +
Sbjct: 124 GATPVTAPEVDLTANVDNLLAAVTPRTKILFLANPNNPTGTYLPATEVARLRAGLRADIL 183

Query: 183 LVIDAAYAEYMNHNDYSAGQELVDRFPNVVMTRTFSKIFALGSVRLGWAYCPAGIADVLN 242
           LVIDAAY E+++ NDYS G ELV+   NVV+ RTFSK++ALG +RLGWAYCP  +A VLN
Sbjct: 184 LVIDAAYTEFVSRNDYSGGIELVEAGDNVVVCRTFSKMYALGGLRLGWAYCPENVAGVLN 243

Query: 243 RVRGPFNVSSAAQIAGVAALEDTAFLERSRSHNIEWREWFVQQVHGLGLKTHPSVTNFVL 302
           RVR PFNV + A  AG+AA  DTA+ E  +SHN  W  W   Q+  LGL   PSV NF+L
Sbjct: 244 RVRNPFNVGAPALAAGLAAFNDTAYAELCKSHNDYWLPWLSGQLAELGLTVVPSVCNFIL 303

Query: 303 VDFAGQTAGKDDAEAARLFLKGRGILVRQMPAYGLPSCLRVTIGTEAEMREVVQALKDFL 362
           V F  + AGK DA AA  FL+ +GI+VR M  YGL  CLR+TIGT  E + VV ALK+F+
Sbjct: 304 VRFP-KDAGK-DAGAADKFLRSKGIIVRAMGGYGLGDCLRITIGTGEENQLVVAALKEFV 361

Query: 363 AA 364
            A
Sbjct: 362 GA 363


Lambda     K      H
   0.319    0.136    0.405 

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: 446
Number of extensions: 14
Number of successful extensions: 3
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: 364
Length of database: 363
Length adjustment: 29
Effective length of query: 335
Effective length of database: 334
Effective search space:   111890
Effective search space used:   111890
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: 49 (23.5 bits)

Align candidate WP_011386328.1 AMB_RS20110 (histidinol-phosphate aminotransferase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.8892.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.8e-92  295.2   0.0    3.1e-92  295.1   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386328.1  AMB_RS20110 histidinol-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386328.1  AMB_RS20110 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.1   0.0   3.1e-92   3.1e-92       1     348 [.       7     359 ..       7     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 295.1 bits;  conditional E-value: 3.1e-92
                                 TIGR01141   1 rekikklepYqpgarelgek.evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakyl 68 
                                               r+ i ++ pY+ g++++ +   ++kL+snE ++gps+k++eal++ + ++hrYpd  a +l++a+ +++
  lcl|NCBI__GCF_000009985.1:WP_011386328.1   7 RPGIMDIRPYVGGESAIEGVdRILKLSSNEGALGPSPKAMEALRAMAPEMHRYPDGGAEDLRKAIGARF 75 
                                               678999*******8887666699********************************************** PP

                                 TIGR01141  69 gveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavl 137
                                               g+++  i+ g+Gsdel+ +l+ra++ pgd+vl++ + + mY++ ak++ga  +++p  +  + +++++l
  lcl|NCBI__GCF_000009985.1:WP_011386328.1  76 GLDASRIVCGAGSDELLGILCRAYAGPGDEVLYSAHGFLMYAIAAKACGATPVTAPEVDL-TANVDNLL 143
                                               ***************************************************999997766.6999**** PP

                                 TIGR01141 138 eaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnl 202
                                               +a++ ++k+ fla+PnnPtG++l + e+ ++ +   +d l V+D AY+eF ++      +el++  +n+
  lcl|NCBI__GCF_000009985.1:WP_011386328.1 144 AAVTPRTKILFLANPNNPTGTYLPATEVARLRAGLrADILLVIDAAYTEFVSRndySGGIELVEAGDNV 212
                                               ***********************************66**************997766789********* PP

                                 TIGR01141 203 vvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkere 271
                                               vv rT+SK+++L+glR+G a++ ++++ +l++vr+p+nv  +al+a++aa +d ++ e +  ++     
  lcl|NCBI__GCF_000009985.1:WP_011386328.1 213 VVCRTFSKMYALGGLRLGWAYCPENVAGVLNRVRNPFNVGAPALAAGLAAFNDTAYAELCKSHNDYWLP 281
                                               ********************************************************************* PP

                                 TIGR01141 272 rlleelkkleglevyeSkaNFvlikvke....daeelleallekgiivRdlksaeglleeclRitvGtr 336
                                               +l  +l++l gl v++S  NF+l+++++    da ++ + l  kgiivR ++ + gl  +clRit+Gt 
  lcl|NCBI__GCF_000009985.1:WP_011386328.1 282 WLSGQLAEL-GLTVVPSVCNFILVRFPKdagkDAGAADKFLRSKGIIVRAMGGY-GL-GDCLRITIGTG 347
                                               *********.8****************9888888888889999***********.85.*********** PP

                                 TIGR01141 337 eenerllealke 348
                                               een+ +++alke
  lcl|NCBI__GCF_000009985.1:WP_011386328.1 348 EENQLVVAALKE 359
                                               **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (363 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: 9.09
//
[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