GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Sinorhizobium meliloti 1021

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate SMc01951 SMc01951 high-affinity branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>lcl|FitnessBrowser__Smeli:SMc01951 SMc01951 high-affinity
           branched-chain amino acid ABC transporter permease
          Length = 300

 Score =  517 bits (1331), Expect = e-151
 Identities = 259/300 (86%), Positives = 280/300 (93%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           MEYFVQQL+NGLTLGSIYG++AIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFL+LT+ 
Sbjct: 1   MEYFVQQLVNGLTLGSIYGMIAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLLLTTF 60

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120
            AG+PV + LL+M+VV ML  +LWNWTIERVAYRPLRGSFRLAPLITAIGMSI LSNFIQ
Sbjct: 61  IAGVPVVLALLIMMVVGMLTAALWNWTIERVAYRPLRGSFRLAPLITAIGMSIVLSNFIQ 120

Query: 121 VTQGPRNKPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180
           VTQGPRNKPIPP+VSSVY    ISVSLKQIII+VITA+LL++FWYIVNRT LGRAQRATE
Sbjct: 121 VTQGPRNKPIPPLVSSVYDLFGISVSLKQIIIVVITAILLSVFWYIVNRTPLGRAQRATE 180

Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVL 240
           QDRKMAALLGV+VD+TIS+TF+MGAALAAVAGTMYLMYYGV  F DGF PGVKAFTAAVL
Sbjct: 181 QDRKMAALLGVDVDRTISVTFIMGAALAAVAGTMYLMYYGVVVFTDGFAPGVKAFTAAVL 240

Query: 241 GGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300
           GGIGSLPGAV GGLLIGLIESLWSAYFTI YKDVATF+ILA VLIFKP+GILGRPEVEKV
Sbjct: 241 GGIGSLPGAVLGGLLIGLIESLWSAYFTIDYKDVATFSILAIVLIFKPSGILGRPEVEKV 300


Lambda     K      H
   0.329    0.143    0.421 

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: 462
Number of extensions: 12
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: 300
Length of database: 300
Length adjustment: 27
Effective length of query: 273
Effective length of database: 273
Effective search space:    74529
Effective search space used:    74529
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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