GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Herbaspirillum seropedicae SmR1

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate HSERO_RS23455 HSERO_RS23455 methylcrotonoyl-CoA carboxylase

Query= metacyc::MONOMER-17283
         (535 letters)



>FitnessBrowser__HerbieS:HSERO_RS23455
          Length = 544

 Score =  740 bits (1910), Expect = 0.0
 Identities = 368/544 (67%), Positives = 423/544 (77%), Gaps = 9/544 (1%)

Query: 1   MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60
           M  I S + P S DFQ N A  Q +  DLRE++A I +GGG   R +H  RGKL  RDR+
Sbjct: 1   MPQIESKLNPRSEDFQNNRAAMQRIVDDLREKIAAIAEGGGQAAREKHLARGKLLPRDRV 60

Query: 61  DTLIDPDSSFLEIGALAAYNVYDEE---------VPAAGIVCGIGRVAGRPVMIIANDAT 111
             L+DP + FLE   LAAY +Y E+          P+AGI+ GIGRVAG+  +I+ NDAT
Sbjct: 61  QMLLDPGTPFLEFSQLAAYGMYREKDRDGQPKDAAPSAGIITGIGRVAGQECVIVCNDAT 120

Query: 112 VKGGTYFPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQA 171
           VKGGTY+P+T KKHLRAQEIA  N LPCIYLVDSGGA LP Q EVFPDRDHFGRIFYNQA
Sbjct: 121 VKGGTYYPMTAKKHLRAQEIAEFNHLPCIYLVDSGGANLPNQDEVFPDRDHFGRIFYNQA 180

Query: 172 QMSAEGIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEE 231
            +SA+GI QIA VMGSCTAGGAYVPAMSDE +IVK   TIFL GPPLVKAATGE V+AEE
Sbjct: 181 NLSAKGIAQIAVVMGSCTAGGAYVPAMSDESIIVKDQATIFLAGPPLVKAATGEVVSAEE 240

Query: 232 LGGADVHTRISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYG 291
           LGG DVHTR+SGVAD+ A DD  ALAI R+IV HL  R+     LR+   PRY  +E+YG
Sbjct: 241 LGGGDVHTRLSGVADHLAQDDTHALAIARNIVGHLNRRKPQPLALRESIEPRYPAQELYG 300

Query: 292 ILPRDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSE 351
           ++P D R+ +DVREVIARIVD S   EFK RYGTTLVCGFAH+ G PVGI+ANNGILFSE
Sbjct: 301 VIPTDTRKPFDVREVIARIVDASEFDEFKARYGTTLVCGFAHLHGMPVGIIANNGILFSE 360

Query: 352 SALKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTV 411
           +A KG HFIELCC R IPL+FLQNITGFMVGK+YEN GIA+ GAK+VTAVS A VPK TV
Sbjct: 361 AAEKGTHFIELCCQRKIPLIFLQNITGFMVGKKYENEGIARHGAKMVTAVSTAKVPKLTV 420

Query: 412 IIGGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTP 471
           IIGGSFGAGNYGMCGRA+ PR LWMWPNARISVMGG QAA+VL T++RD + ARG   + 
Sbjct: 421 IIGGSFGAGNYGMCGRAFSPRFLWMWPNARISVMGGEQAASVLATVKRDGIEARGGSWSA 480

Query: 472 EEQERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFG 531
           EE+  F  PI A+YE +GHPYYASARLWDDGVIDP +TR+VLALGL+AA  AP++ TRFG
Sbjct: 481 EEEAAFKEPIRAQYETQGHPYYASARLWDDGVIDPADTRQVLALGLSAALNAPIEETRFG 540

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


Lambda     K      H
   0.322    0.139    0.423 

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: 979
Number of extensions: 43
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: 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 (21.9 bits)
S2: 52 (24.6 bits)

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

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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:

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