Aligments for a candidate for fruI in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__azobra:AZOBR_RS32325 AZOBR_RS32325 PTS fructose
           transporter subunit IIA
          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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, or view the source code.

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 catabolism of small carbon sources