GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Herbaspirillum seropedicae SmR1

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate HSERO_RS23455 HSERO_RS23455 methylcrotonoyl-CoA carboxylase

Query= reanno::SB2B:6937191
         (535 letters)



>FitnessBrowser__HerbieS:HSERO_RS23455
          Length = 544

 Score =  809 bits (2089), Expect = 0.0
 Identities = 395/544 (72%), Positives = 455/544 (83%), Gaps = 9/544 (1%)

Query: 1   MTQLTSRVNPRSDEFKQKHDAMAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARV 60
           M Q+ S++NPRS++F+    AM  +V DL++K+A I +GGG  A E+HL+RGKL PR RV
Sbjct: 1   MPQIESKLNPRSEDFQNNRAAMQRIVDDLREKIAAIAEGGGQAAREKHLARGKLLPRDRV 60

Query: 61  EKLLDPGSPFLELSQFAAFEVYDED---------VPAAGIIAGIGRVSGVECMIIANDAT 111
           + LLDPG+PFLE SQ AA+ +Y E           P+AGII GIGRV+G EC+I+ NDAT
Sbjct: 61  QMLLDPGTPFLEFSQLAAYGMYREKDRDGQPKDAAPSAGIITGIGRVAGQECVIVCNDAT 120

Query: 112 VKGGTYYPITVKKHLRAQAIAERCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQA 171
           VKGGTYYP+T KKHLRAQ IAE  HLPCIYLVDSGGANLP QDEVFPDRDHFGRIF+NQA
Sbjct: 121 VKGGTYYPMTAKKHLRAQEIAEFNHLPCIYLVDSGGANLPNQDEVFPDRDHFGRIFYNQA 180

Query: 172 RMSAKGIPQIAVVMGLCTAGGAYVPAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEE 231
            +SAKGI QIAVVMG CTAGGAYVPAM+DESIIV++Q TIFLAGPPLVKAATGE VSAEE
Sbjct: 181 NLSAKGIAQIAVVMGSCTAGGAYVPAMSDESIIVKDQATIFLAGPPLVKAATGEVVSAEE 240

Query: 232 LGGGDVHTKISGVADHLAQNDEHALELARKAVSRLNHQKQVELQLSKVKPPKYDINELYG 291
           LGGGDVHT++SGVADHLAQ+D HAL +AR  V  LN +K   L L +   P+Y   ELYG
Sbjct: 241 LGGGDVHTRLSGVADHLAQDDTHALAIARNIVGHLNRRKPQPLALRESIEPRYPAQELYG 300

Query: 292 IVGTDLKKPFDVKEVIARIVDDSDFDEFKANYGTTLVCGFARIHGYPVGIVANNGILFSE 351
           ++ TD +KPFDV+EVIARIVD S+FDEFKA YGTTLVCGFA +HG PVGI+ANNGILFSE
Sbjct: 301 VIPTDTRKPFDVREVIARIVDASEFDEFKARYGTTLVCGFAHLHGMPVGIIANNGILFSE 360

Query: 352 SAQKGAHFIELCCQRKIPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTV 411
           +A+KG HFIELCCQRKIPL+FLQNITGFMVGKKYE+EGIA+HGAKMVTAVS A VPK TV
Sbjct: 361 AAEKGTHFIELCCQRKIPLIFLQNITGFMVGKKYENEGIARHGAKMVTAVSTAKVPKLTV 420

Query: 412 LIGGSYGAGNYGMCGRAFEPTLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSA 471
           +IGGS+GAGNYGMCGRAF P  +WMWPNARISVMGGEQAA VLATV++DG+  +G + SA
Sbjct: 421 IIGGSFGAGNYGMCGRAFSPRFLWMWPNARISVMGGEQAASVLATVKRDGIEARGGSWSA 480

Query: 472 EEEAKFKAPIIAQYDKEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPIEETRFG 531
           EEEA FK PI AQY+ +GHPY+ASARLWDDG+IDPA TR VL L +SAALNAPIEETRFG
Sbjct: 481 EEEAAFKEPIRAQYETQGHPYYASARLWDDGVIDPADTRQVLALGLSAALNAPIEETRFG 540

Query: 532 VFRM 535
           VFR+
Sbjct: 541 VFRI 544


Lambda     K      H
   0.320    0.137    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: 1009
Number of extensions: 42
Number of successful extensions: 2
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: 535
Length of database: 544
Length adjustment: 35
Effective length of query: 500
Effective length of database: 509
Effective search space:   254500
Effective search space used:   254500
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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:

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:

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:

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:

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