GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Limnohabitans curvus MWH-C5

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_108401790.1 B9Z44_RS04225 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_003063475.1:WP_108401790.1
          Length = 309

 Score =  273 bits (698), Expect = 4e-78
 Identities = 142/302 (47%), Positives = 199/302 (65%), Gaps = 9/302 (2%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M+  +QQ++NGL LGS+Y LVA+GYTMVYGII +INFAHG++ M+G   +  V  +L  +
Sbjct: 1   MDVLLQQVINGLVLGSMYALVALGYTMVYGIINLINFAHGEVLMIGALCSWSVIGLLQPL 60

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120
               P  VLLL+ +V+A +  +  N+ IE++AYRPLR + +LAPLITAIGMSI L     
Sbjct: 61  MPDTPGWVLLLISMVLASIAAAALNYAIEKIAYRPLRNAPKLAPLITAIGMSILLQTLAM 120

Query: 121 VTQGPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179
           +   P  KP P ++ +  ++ G   ++  Q++I+ +TAV L +  ++VNRT LGRA RAT
Sbjct: 121 IVWKPNYKPFPTLLPTTPFEIGEAVITPTQLMILGLTAVALAVLSWLVNRTKLGRAMRAT 180

Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239
            ++ ++A+L+GV  D  IS TF++GA LA +AG M+ M YG A    GF PG+KAFTAAV
Sbjct: 181 AENPRVASLMGVKPDVVISATFIIGAVLATIAGVMWAMNYGTAHHAMGFLPGLKAFTAAV 240

Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAY--------FTIAYKDVATFAILAFVLIFKPTGI 291
            GGIG+L GAV GGLL+GLIES+ S Y            Y D+  F +L   L  +P+G+
Sbjct: 241 FGGIGNLGGAVVGGLLLGLIESIGSGYLGELTGGVLGSHYTDILAFVVLIITLTLRPSGL 300

Query: 292 LG 293
           LG
Sbjct: 301 LG 302


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: 351
Number of extensions: 18
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: 309
Length adjustment: 27
Effective length of query: 273
Effective length of database: 282
Effective search space:    76986
Effective search space used:    76986
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 24 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