GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Azospirillum brasilense Sp245

Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate AZOBR_RS32325 AZOBR_RS32325 PTS fructose transporter subunit IIA

Query= reanno::azobra:AZOBR_RS32325
         (846 letters)



>FitnessBrowser__azobra:AZOBR_RS32325
          Length = 846

 Score = 1639 bits (4243), Expect = 0.0
 Identities = 846/846 (100%), Positives = 846/846 (100%)

Query: 1   MAPDANTAIMPTDLLRPELLRLSASPAGKEEAIREAAQLLIAAGCIDSAYAASMLRREAV 60
           MAPDANTAIMPTDLLRPELLRLSASPAGKEEAIREAAQLLIAAGCIDSAYAASMLRREAV
Sbjct: 1   MAPDANTAIMPTDLLRPELLRLSASPAGKEEAIREAAQLLIAAGCIDSAYAASMLRREAV 60

Query: 61  ANTFLGHGVAIPHGMVEDRGMVRRSGIAVLQVPGGIAWNPGQTAHLVVAIAAQSDAHIAV 120
           ANTFLGHGVAIPHGMVEDRGMVRRSGIAVLQVPGGIAWNPGQTAHLVVAIAAQSDAHIAV
Sbjct: 61  ANTFLGHGVAIPHGMVEDRGMVRRSGIAVLQVPGGIAWNPGQTAHLVVAIAAQSDAHIAV 120

Query: 121 LRRLTRLMQDEARLTALFTVTDPAALAAALGEDAPVAAPATPGGDLAERFDWVVDYPTGL 180
           LRRLTRLMQDEARLTALFTVTDPAALAAALGEDAPVAAPATPGGDLAERFDWVVDYPTGL
Sbjct: 121 LRRLTRLMQDEARLTALFTVTDPAALAAALGEDAPVAAPATPGGDLAERFDWVVDYPTGL 180

Query: 181 HARPATAWVETARASAARIQVRHGDLVADAKALVALLQLGLRAGDSVVVSAEGDDAVAAL 240
           HARPATAWVETARASAARIQVRHGDLVADAKALVALLQLGLRAGDSVVVSAEGDDAVAAL
Sbjct: 181 HARPATAWVETARASAARIQVRHGDLVADAKALVALLQLGLRAGDSVVVSAEGDDAVAAL 240

Query: 241 ARMKATITRLTAREKADAAAAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIGPVHVLPR 300
           ARMKATITRLTAREKADAAAAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIGPVHVLPR
Sbjct: 241 ARMKATITRLTAREKADAAAAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIGPVHVLPR 300

Query: 301 AAVSVPDEPVPLIEGGDRLHEALSLTRQNLKALADDTARRLGPSEAAIFAAQAEILNDTD 360
           AAVSVPDEPVPLIEGGDRLHEALSLTRQNLKALADDTARRLGPSEAAIFAAQAEILNDTD
Sbjct: 301 AAVSVPDEPVPLIEGGDRLHEALSLTRQNLKALADDTARRLGPSEAAIFAAQAEILNDTD 360

Query: 361 LVTLACQLMVEGHGVAWSWHQAVERTAAGLAALDNPVLAARAADLRDVGQRVLARIDPAL 420
           LVTLACQLMVEGHGVAWSWHQAVERTAAGLAALDNPVLAARAADLRDVGQRVLARIDPAL
Sbjct: 361 LVTLACQLMVEGHGVAWSWHQAVERTAAGLAALDNPVLAARAADLRDVGQRVLARIDPAL 420

Query: 421 RTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAILARTLGLPAMV 480
           RTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAILARTLGLPAMV
Sbjct: 421 RTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAILARTLGLPAMV 480

Query: 481 AGGAALMELANGTPAILDGQSGRLHLSPAAADIADARAWIAREEARKAEEEARRGLPART 540
           AGGAALMELANGTPAILDGQSGRLHLSPAAADIADARAWIAREEARKAEEEARRGLPART
Sbjct: 481 AGGAALMELANGTPAILDGQSGRLHLSPAAADIADARAWIAREEARKAEEEARRGLPART 540

Query: 541 RDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDEQYETYRGMLTA 600
           RDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDEQYETYRGMLTA
Sbjct: 541 RDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDEQYETYRGMLTA 600

Query: 601 LEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLRRPELLETQLRALYRAAKD 660
           LEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLRRPELLETQLRALYRAAKD
Sbjct: 601 LEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLRRPELLETQLRALYRAAKD 660

Query: 661 GGAKDGGALSIMFPMITALGEVQALRAACERIRAELDAPAVPLGIMVEVPAAAIQADVLA 720
           GGAKDGGALSIMFPMITALGEVQALRAACERIRAELDAPAVPLGIMVEVPAAAIQADVLA
Sbjct: 661 GGAKDGGALSIMFPMITALGEVQALRAACERIRAELDAPAVPLGIMVEVPAAAIQADVLA 720

Query: 721 RHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPAVLRLIRLTVEGAERHGRWVGVCG 780
           RHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPAVLRLIRLTVEGAERHGRWVGVCG
Sbjct: 721 RHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPAVLRLIRLTVEGAERHGRWVGVCG 780

Query: 781 GIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRLRGSDLSALKDAAQRALDCETADAVRA 840
           GIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRLRGSDLSALKDAAQRALDCETADAVRA
Sbjct: 781 GIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRLRGSDLSALKDAAQRALDCETADAVRA 840

Query: 841 LDGGAA 846
           LDGGAA
Sbjct: 841 LDGGAA 846


Lambda     K      H
   0.319    0.134    0.387 

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: 2536
Number of extensions: 113
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: 846
Length of database: 846
Length adjustment: 42
Effective length of query: 804
Effective length of database: 804
Effective search space:   646416
Effective search space used:   646416
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: 56 (26.2 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