GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Mesorhizobium ciceri WSM1271

Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate YP_004143814.1 Mesci_4655 polar amino acid ABC transporter inner membrane subunit

Query= uniprot:Q31RN9
         (396 letters)



>NCBI__GCF_000185905.1:YP_004143814.1
          Length = 385

 Score =  216 bits (551), Expect = 7e-61
 Identities = 140/410 (34%), Positives = 213/410 (51%), Gaps = 91/410 (22%)

Query: 16  AWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWT--------------VLVD 61
           AW+R+NL +S  ++ +T++ + ++  ++ ++  W    A WT              +  D
Sbjct: 28  AWVRKNLIASTGDTILTIVGIALVAMILPQIINWAFINAVWTGPDRTVCATVAQGGIQPD 87

Query: 62  NWT------------LFFVGRYPAAEQWR----LWLWLGLLSPTLGLTWGCLATGSHRWQ 105
            WT             F +GRYP  E+WR      L++ LL P L               
Sbjct: 88  GWTGACWAFVNAKFGQFMLGRYPIEERWRPILVAILFVALLVPML--------------- 132

Query: 106 RRSLWGWAGLAAAIAGIPLPWFPHKLGLAAIAATVPAASWLAQRCRGQAWLRFLPTLWGV 165
                             +P  P K GL A+                         L+ V
Sbjct: 133 ------------------MPKVPRK-GLNAVL------------------------LFFV 149

Query: 166 LFLVGLWLLQGGL-GLRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIR 224
           L +V   LL GG+ GL  V ++ W GLL+TL+ + + +  SLPLGI+LALGR+S +P I+
Sbjct: 150 LPIVAFVLLVGGMFGLPHVETSLWGGLLVTLSLSFVGIAVSLPLGIVLALGRRSKMPIIK 209

Query: 225 WLSVTYIELFRGLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRG 284
            L V +IE  RG+PL+T+LFF  VM+PL L      D+ LRA++G+++F +AY+AE VRG
Sbjct: 210 TLCVVFIETVRGIPLITVLFFASVMLPLFLPEGVSFDKFLRALIGVSLFAAAYMAEVVRG 269

Query: 285 GLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLL 344
           GLQAIP+GQ+E A +LGL  +Q   FIV+PQAL++ IP IV  F+ + +DT+L+ I+ + 
Sbjct: 270 GLQAIPKGQYEGADSLGLGYWQKMYFIVMPQALKLVIPGIVNTFIGMFKDTSLVIIISMF 329

Query: 345 ELLGISRSIL--ANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392
           +LLGI +     AN A         +F   ++WL C+G+++ S   E+RL
Sbjct: 330 DLLGIVKQNFSDANWATAQTARSGLIFAAFVFWLFCFGMSRYSMYTERRL 379


Lambda     K      H
   0.329    0.142    0.471 

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: 416
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 396
Length of database: 385
Length adjustment: 31
Effective length of query: 365
Effective length of database: 354
Effective search space:   129210
Effective search space used:   129210
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: 50 (23.9 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